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@article{Calle2003,
author = {Calle, Eugene E. and Rodriguez, Carmen and Walker-Thurmond, Kimberly and Thun, Michael J.},
doi = {10.1056/NEJMoa0810625)},
file = {:home/riku/Documents/Mendeley Desktop/Calle et al/Calle et al.{\_}2003{\_}Overweight, obesity, and mortality from cancer in a prospectively studied cofort of U.S. adults.pdf:pdf},
journal = {N. Engl. J. Med.},
keywords = {obesity},
mendeley-tags = {obesity},
number = {17},
pages = {1625--1638},
title = {{Overweight, obesity, and mortality from cancer in a prospectively studied cofort of U.S. adults}},
volume = {348},
year = {2003}
}
@article{Scuteri2007,
abstract = {The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 showed the strongest association with BMI (p = 8.6 x10(-7)), hip circumference (p = 3.4 x 10(-8)), and weight (p = 9.1 x 10(-7)). In Sardinia, homozygotes for the rare "G" allele of this SNP (minor allele frequency = 0.46) were 1.3 BMI units heavier than homozygotes for the common "A" allele. Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 x 10(-6)). Homozygotes for the rare "A" allele of this SNP (minor allele frequency = 0.12) were 1.8 BMI units heavier than homozygotes for the common "G" allele. To replicate our findings, we genotyped these two SNPs in the GenNet study. In European Americans (N = 1,496) and in Hispanic Americans (N = 839), we replicated significant association between rs9930506 in the FTO gene and BMI (p-value for meta-analysis of European American and Hispanic American follow-up samples, p = 0.001), weight (p = 0.001), and hip circumference (p = 0.0005). We did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although we found that in European Americans, Hispanic Americans, and African Americans, homozygotes for the rare "A" allele were, on average, 1.0-3.0 BMI units heavier than homozygotes for the more common "G" allele. In summary, we have completed a whole genome-association scan for three obesity-related quantitative traits and report that common genetic variants in the FTO gene are associated with substantial changes in BMI, hip circumference, and body weight. These changes could have a significant impact on the risk of obesity-related morbidity in the general population.},
author = {Scuteri, Angelo and Sanna, Serena and Chen, Wei Min and Uda, Manuela and Albai, Giuseppe and Strait, James and Najjar, Samer and Nagaraja, Ramaiah and Orr??, Marco and Usala, Gianluca and Dei, Mariano and Lai, Sandra and Maschio, Andrea and Busonero, Fabio and Mulas, Antonella and Ehret, Georg B. and Fink, Ashley A. and Weder, Alan B. and Cooper, Richard S. and Galan, Pilar and Chakravarti, Aravinda and Schlessinger, David and Cao, Antonio and Lakatta, Edward and Abecasis, Gon??alo R.},
doi = {10.1371/journal.pgen.0030115},
file = {:home/riku/Documents/Mendeley Desktop/Scuteri et al/Scuteri et al.{\_}2007{\_}Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits.pdf:pdf},
isbn = {1553-7404},
issn = {15537390},
journal = {PLoS Genet.},
keywords = {FTO,GWAS,obesity},
mendeley-tags = {FTO,GWAS,obesity},
number = {7},
pages = {1200--1210},
pmid = {17658951},
title = {{Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits}},
volume = {3},
year = {2007}
}
@article{Barsh2002,
abstract = {The homeostatic regulation of adiposity is a physiological concept that originated nearly 70 years ago, the genetic foundations of which have just begun to emerge. A key element of this concept is the existence of one or more humoral mediators, which circulate at levels that reflect body fat stores and which signal through neuronal receptors to elicit appropriate behavioural and metabolic responses over short time periods. Initial insights into adiposity regulation came from the positional cloning of mouse obesity mutations, but the field is now poised to address specific physiological questions using more sophisticated genetic approaches.},
author = {Barsh, Gregory S and Schwartz, Michael W},
doi = {10.1038/nrg862},
file = {:home/riku/Documents/Mendeley Desktop/Barsh, Schwartz/Barsh, Schwartz{\_}2002{\_}Genetic approaches to studying energy balance perception and integration.pdf:pdf},
isbn = {1471-0056 (Print)$\backslash$n1471-0056 (Linking)},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
keywords = {Adipose Tissue,Adipose Tissue: metabolism,Animals,Biological,Brown,Brown: physiology,Energy Metabolism,Energy Metabolism: physiology,Humans,Models,Obesity,Obesity: etiology,Obesity: metabolism,Proteins,Proteins: genetics,Proteins: physiology,obesity},
mendeley-tags = {obesity},
number = {8},
pages = {589--600},
pmid = {12154382},
title = {{Genetic approaches to studying energy balance: perception and integration.}},
volume = {3},
year = {2002}
}
@article{WHO2014,
abstract = {Description of the global burden of NCDs, their risk factors and determinants},
author = {{World Health Organisation}},
doi = {ISBN 9789241564854},
file = {:home/riku/Documents/Mendeley Desktop/World Health Organisation/World Health Organisation{\_}2014{\_}Global status report on noncommunicable diseases 2014.pdf:pdf},
isbn = {978 92 4 156485 4},
journal = {World Health},
keywords = {obesity},
mendeley-tags = {obesity},
pages = {176},
title = {{Global status report on noncommunicable diseases 2014}},
year = {2014}
}
@article{Friedman1998,
abstract = {The assimilation, storage and use of energy from nutrients constitute a homeostatic system that is essential for life. In vertebrates, the ability to store sufficient quantities of energy-dense triglyceride in adipose tissue allows survival during the frequent periods of food deprivation encountered during evolution. However, the presence of excess adipose tissue can be maladaptive. A complex physiological system has evolved to regulate fuel stores and energy balance at an optimum level. Leptin, a hormone secreted by adipose tissue, and its receptor are integral components of this system. Leptin also signals nutritional status to several other physiological systems and modulates their function. Here we review the role of leptin in the control of body weight and its relevance to the pathogenesis of obesity.},
author = {Friedman, J M and Halaas, J L},
doi = {10.1038/27376},
file = {:home/riku/Documents/Mendeley Desktop/Friedman, Halaas/Friedman, Halaas{\_}1998{\_}Leptin and the regulation of body weight in mammals.pdf:pdf},
isbn = {0028-0836},
issn = {0028-0836},
journal = {Nature},
keywords = {obesity},
mendeley-tags = {obesity},
number = {6704},
pages = {763--770},
pmid = {9796811},
title = {{Leptin and the regulation of body weight in mammals.}},
volume = {395},
year = {1998}
}
@article{Jones1997,
abstract = {Black women with breast cancer are less likely than white women to be diagnosed while their disease is still at a localized stage. Racial differences in the prevalence of obesity in the United States have also been documented. This study was undertaken to determine the extent to which the observed racial difference in stage at diagnosis of breast cancer could be explained by racial differences in obesity, specifically severe obesity. This was a population-based, retrospective study of 145 black women and 177 white women in Connecticut who were diagnosed with breast cancer between January 1987 and March 1989. Severe obesity was associated with both race and stage at diagnosis: Black women were significantly more likely than white women to be severely obese (26{\%} vs. 7{\%}, respectively), and severe obesity was significantly associated with diagnosis at TNM stage II or greater (multivariate-adjusted odds ratio = 3.10, 95{\%} confidence interval (CI) 1.28-7.52). Adjustment for severe obesity in a logistic regression model reduced the risk of later stage at diagnosis in blacks relative to whites by 33{\%}, from an odds ratio of 1.98 (95{\%} CI 1.22-3.19) to one of 1.66 (95{\%} CI 1.01-2.73). The higher prevalence of severe obesity among black women may play an important role in explaining their relative disadvantage in stage at diagnosis of breast cancer.},
author = {Jones, B A and Kasi, S V and Curnen, M G and Owens, P H and Dubrow, R},
file = {:home/riku/Documents/Mendeley Desktop/Jones et al/Jones et al.{\_}1997{\_}Severe obesity as an explanatory factor for the blackwhite difference in stage at diagnosis of breast cancer.pdf:pdf},
isbn = {0002-9262 (Print)},
issn = {0002-9262},
journal = {Am. J. Epidemiol.},
number = {5},
pages = {394--404},
pmid = {9290499},
title = {{Severe obesity as an explanatory factor for the black/white difference in stage at diagnosis of breast cancer.}},
volume = {146},
year = {1997}
}
@article{Irizarry2003,
abstract = {SUMMARY In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip R system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of five MGU74A mouse GeneChip R arrays, part of the data from an extensive spike-in study conducted by Gene Logic and Wyeth's Genetics Institute involving 95 HG-U95A human GeneChip R arrays; and part of a dilution study conducted by Gene Logic involving 75 HG-U95A GeneChip R arrays. We display some familiar features of the perfect match and mismatch probe (P M and M M) values of these data, and examine the variance–mean relationship with probe-level data from probes believed to be defective, and so delivering noise only. We explain why we need to normalize the arrays to one another using probe level intensities. We then examine the behavior of the P M and M M using spike-in data and assess three commonly used summary measures: Affymetrix's (i) average difference (AvDiff) and (ii) MAS 5.0 signal, and (iii) the Li and Wong multiplicative model-based expression index (MBEI). The exploratory data analyses of the probe level data motivate a new summary measure that is a robust multi-array average (RMA) of background-adjusted, normalized, and log-transformed P M values. We evaluate the four expression summary measures using the dilution study data, assessing their behavior in terms of bias, variance and (for MBEI and RMA) model fit. Finally, we evaluate the algorithms in terms of their ability to detect known levels of differential expression using the spike-in data. We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities.},
author = {Irizarry, Rafael A and Hobbs, Bridget and Collin, Francois and Beazer-Barclay, Yasmin D and Antonellis, Kristen J and Scherf, Uwe and Speed, Terence P},
doi = {10.1093/biostatistics/4.2.249},
file = {:home/riku/Documents/Mendeley Desktop/Irizarry et al/Irizarry et al.{\_}2003{\_}Exploration, normalization, and summaries of high density oligonucleotide array probe level data.pdf:pdf},
isbn = {1465-4644 (Print) 1465-4644 (Linking)},
issn = {1465-4644},
journal = {Biostatistics},
number = {2},
pages = {249--264},
pmid = {12925520},
title = {{Exploration, normalization, and summaries of high density oligonucleotide array probe level data}},
volume = {4},
year = {2003}
}
@article{Gatza2011,
abstract = {INTRODUCTION: Breast cancer heterogeneity occurs as a consequence of the dysregulation of numerous oncogenic pathways as well as many non-genetic factors, including tumor microenvironmental stresses such as hypoxia, lactic acidosis, and glucose deprivation. Although the importance of these non-genetic factors is well recognized, it is not clear how to integrate these factors within the genetic framework of cancer as the next logical step in understanding tumor heterogeneity.$\backslash$n$\backslash$nMETHODS: We report here the development of a series of gene expression signatures to measure the influences of microenvironmental stresses. The pathway activities of hypoxia, lactic acidosis, acidosis and glucose deprivation were investigated in a collection of 1,143 breast tumors, which have been separated into 17 breast tumor subgroups defined by their distinct patterns of oncogenic pathways. A validation dataset comprised of 547 breast tumors was also used to confirm the major findings, and representative breast cancer cell lines were utilized to validate in silico results and mechanistic studies.$\backslash$n$\backslash$nRESULTS: Through the integrative pathway analysis of microenvironmental stresses and oncogenic events in breast tumors, we identified many known and novel correlations between these two sources of tumor heterogeneity. Focusing on differences between two human epidermal growth factor receptor 2 (HER2)-related subgroups, previously identified based on patterns of oncogenic pathway activity, we determined that these subgroups differ with regards to tumor microenvironmental signatures, including hypoxia. We further demonstrate that each of these subgroups have features consistent with basal and luminal breast tumors including patterns of oncogenic signaling pathways, expression of subtype specific genes, and cellular mechanisms that regulate the hypoxia response. Importantly, we also demonstrate that the correlated pattern of hypoxia-related gene expression and basal-associated gene expression are consistent across HER2-related tumors whether we analyze the tumors as a function of our pathway-based classification scheme, using the intrinsic gene list (ERBB2+), or based on HER2 IHC status. Our results demonstrate a cell lineage-specific phenomenon in which basal-like tumors, HER2-related tumors with high hypoxia, as well as normal basal epithelial cells express increased mRNA levels of HIF-1$\alpha$ compared to luminal types and silencing of HIF-1$\alpha$ results in decreased expression of hypoxia-induced genes.$\backslash$n$\backslash$nCONCLUSIONS: This study demonstrates differences in microenvironmental conditions in HER2-related subgroups defined by distinct oncogenic pathway activities, and provides a mechanistic explanation for differences in the observed hypoxia response between these subgroups. Collectively, these data demonstrate the potential of a pathway-based classification strategy as a framework to integrate genetic and non-genetic factors to investigate the basis of tumor heterogeneity.},
author = {Gatza, Michael L and Kung, Hsiu-Ni and Blackwell, Kimberly L and Dewhirst, Mark W and Marks, Jeffrey R and Chi, Jen-Tsan},
doi = {10.1186/bcr2899},
file = {:home/riku/Documents/Mendeley Desktop/Gatza et al/Gatza et al.{\_}2011{\_}Analysis of tumor environmental response and oncogenic pathway activation identifies distinct basal and luminal featur.pdf:pdf},
issn = {1465-5411},
journal = {Breast Cancer Res.},
number = {3},
pages = {R62},
pmid = {21672245},
publisher = {BioMed Central Ltd},
title = {{Analysis of tumor environmental response and oncogenic pathway activation identifies distinct basal and luminal features in HER2-related breast tumor subtypes}},
volume = {13},
year = {2011}
}
@misc{Løning2013a,
abstract = {Following their successful implementation for the treatment of metastatic breast cancer, the 'third-generation' aromatase inhibitors (anastrozole, letrozole, and exemestane) have now become standard adjuvant endocrine treatment for postmenopausal estrogen receptor-positive breast cancers. These drugs are characterized by potent aromatase inhibition, causing {\textgreater}98{\%} inhibition of estrogen synthesis in vivo. A recent meta-analysis found no difference in anti-tumor efficacy between these three compounds. As of today, aromatase inhibitor monotherapy and sequential treatment using tamoxifen followed by an aromatase inhibitor for a total of 5 years are considered equipotent treatment options. However, current trials are addressing the potential benefit of extending treatment duration beyond 5 years. Regarding side effects, aromatase inhibitors are not found associated with enhanced risk of cardiovascular disease, and enhanced bone loss is prevented by adding bisphosphonates in concert for those at danger of developing osteoporosis. However, arthralgia and carpal tunnel syndrome preclude drug administration among a few patients. While recent findings have questioned the use of aromatase inhibitors among overweight and, in particular, obese patients, this problem seems to focus on premenopausal patients treated with an aromatase inhibitor and an LH-RH analog in concert, questioning the efficacy of LH-RH analogs rather than aromatase inhibitors among overweight patients. Finally, recent findings revealing a benefit from adding the mTOR inhibitor everolimus to endocrine treatment indicate targeted therapy against defined growth factor pathways to be a way forward, by reversing acquired resistance to endocrine therapy.},
author = {L{\o}ning, Per Eystein and Eikesdal, Hans Petter},
booktitle = {Endocr. Relat. Cancer},
doi = {10.1530/ERC-13-0099},
file = {:home/riku/Documents/Mendeley Desktop/L{\o}ning, Eikesdal/L{\o}ning, Eikesdal{\_}2013{\_}Aromatase inhibition 2013 Clinical state of the art and questions that remain to be solved.pdf:pdf},
isbn = {1479-6821 (Electronic)$\backslash$n1351-0088 (Linking)},
issn = {13510088},
keywords = {Adjuvant therapy,Aromatase inhibitors,Breast cancer,Endocrine therapy,Resistance},
number = {4},
pmid = {23625614},
title = {{Aromatase inhibition 2013: Clinical state of the art and questions that remain to be solved}},
volume = {20},
year = {2013}
}
@article{Hanahan2011,
abstract = {The hallmarks of cancer comprise six biological capabilities acquired during the multistep development of human tumors. The hallmarks constitute an organizing principle for rationalizing the complexities of neoplastic disease. They include sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis. Underlying these hallmarks are genome instability, which generates the genetic diversity that expedites their acquisition, and inflammation, which fosters multiple hallmark functions. Conceptual progress in the last decade has added two emerging hallmarks of potential generality to this list - reprogramming of energy metabolism and evading immune destruction. In addition to cancer cells, tumors exhibit another dimension of complexity: they contain a repertoire of recruited, ostensibly normal cells that contribute to the acquisition of hallmark traits by creating the "tumor microenvironment." Recognition of the widespread applicability of these concepts will increasingly affect the development of new means to treat human cancer. ?? 2011 Elsevier Inc.},
author = {Hanahan, Douglas and Weinberg, Robert A.},
doi = {10.1016/j.cell.2011.02.013},
file = {:home/riku/Documents/Mendeley Desktop/Hanahan, Weinberg/Hanahan, Weinberg{\_}2011{\_}Hallmarks of cancer The next generation.pdf:pdf},
isbn = {0026201009680},
issn = {00928674},
journal = {Cell},
keywords = {Key Paper},
mendeley-tags = {Key Paper},
number = {5},
pages = {646--674},
pmid = {21376230},
publisher = {Elsevier Inc.},
title = {{Hallmarks of cancer: The next generation}},
volume = {144},
year = {2011}
}
@article{West2001,
abstract = {Prognostic and predictive factors are indispensable tools in the treatment of patients with neoplastic disease. For the most part, such factors rely on a few specific cell surface, histological, or gross pathologic features. Gene expression assays have the potential to supplement what were previously a few distinct features with many thousands of features. We have developed Bayesian regression models that provide predictive capability based on gene expression data derived from DNA microarray analysis of a series of primary breast cancer samples. These patterns have the capacity to discriminate breast tumors on the basis of estrogen receptor status and also on the categorized lymph node status. Importantly, we assess the utility and validity of such models in predicting the status of tumors in crossvalidation determinations. The practical value of such approaches relies on the ability not only to assess relative probabilities of clinical outcomes for future samples but also to provide an honest assessment of the uncertainties associated with such predictive classifications on the basis of the selection of gene subsets for each validation analysis. This latter point is of critical importance in the ability to apply these methodologies to clinical assessment of tumor phenotype.},
author = {West, M and Blanchette, C and Dressman, H and Huang, E and Ishida, S and Spang, R and Zuzan, H and Olson, J A and Marks, J R and Nevins, J R},
doi = {10.1073/pnas.201162998},
file = {:home/riku/Documents/Mendeley Desktop/West et al/West et al.{\_}2001{\_}Predicting the clinical status of human breast cancer by using gene expression profiles.pdf:pdf},
isbn = {0027-8424 LA - eng},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
keywords = {Bacillus anthracis,Breast Neoplasms,Breast Neoplasms: enzymology,Breast Neoplasms: genetics,Breast Neoplasms: pathology,Breast Neoplasms: surgery,Enzymes,Enzymes: genetics,Estrogen,Estrogen: analysis,Female,Humans,Lymph Node Excision,Lymph Nodes,Lymph Nodes: pathology,Multigene Family,Oligonucleotide Array Sequence Analysis,Phenotype,Predictive Value of Tests,Probability,Receptors,Reproducibility of Results},
number = {20},
pages = {11462--11467},
pmid = {11562467},
title = {{Predicting the clinical status of human breast cancer by using gene expression profiles.}},
volume = {98},
year = {2001}
}
@article{Feliciano2017,
author = {Feliciano, Elizabeth M Cespedes and Kwan, Marilyn L and Kushi, Lawrence H and Chen, Wendy Y},
doi = {10.1002/cncr.30637},
file = {:home/riku/Documents/Mendeley Desktop/Feliciano et al/Feliciano et al.{\_}2017{\_}Body Mass Index , PAM50 Subtype , Recurrence , and Survival Among Patients With Nonmetastatic Breast Cancer.pdf:pdf},
journal = {Cancer},
keywords = {50,body mass index,breast cancer subtype,gene expression assay,molecular classification,mortality,obesity,pam50,prediction analysis of microarray,recurrence,survival},
pages = {2535--2542},
title = {{Body Mass Index , PAM50 Subtype , Recurrence , and Survival Among Patients With Nonmetastatic Breast Cancer}},
volume = {123},
year = {2017}
}
@incollection{Smyth2005,
abstract = {Abstract A survey is given of differential expression analyses using the linear modeling features of the limma package. The chapter starts with the simplest replicated designs and progresses through experiments with two or more groups, direct designs, factorial designs ...},
archivePrefix = {arXiv},
arxivId = {16495579},
author = {Smyth, G K},
booktitle = {Bioinforma. Comput. Biol. Solut. Using R Bioconductor},
doi = {10.1007/0-387-29362-0_23},
eprint = {16495579},
file = {:home/riku/Documents/Mendeley Desktop/Smyth/Smyth{\_}2005{\_}Limma linear models for microarray data.pdf:pdf},
isbn = {1431-8776},
issn = {1544-6115},
pages = {397--420},
pmid = {16495579},
title = {{Limma: linear models for microarray data}},
year = {2005}
}
@article{Dawood2008,
abstract = {PURPOSE: The purpose of this retrospective study was to determine the association and prognostic value of body mass index (BMI) at the time of initial diagnosis in patients with locally advanced breast cancer (LABC). The analysis includes the subsets of inflammatory (IBC) and noninflammatory (non-IBC LABC) breast cancer. EXPERIMENTAL DESIGN: We identified 602 patients who had LABC treated on prospective clinical trials. BMI was divided into three groups: (a) {\textless} or =24.9 (normal/underweight), (b) 25.0 to 29.9 (overweight), and (c) {\textgreater} or =30 (obese). Kaplan-Meier product limit method was used to estimate survival outcomes. Cox proportional hazards were used to determine associations between survival and BMI and to test for an interaction between BMI and breast cancer type. RESULTS: Eighty-two percent had non-IBC LABC and 18{\%} had IBC. Obese patients tended to have a higher incidence of IBC compared with overweight and normal/underweight groups (P = 0.01). Median follow up was 6 years for all patients. Median overall survival (OS) and recurrence-free survival (RFS) were 8.8 and 5.9 years, respectively. Patients with LABC who were obese or overweight had a significantly worse OS and RFS (P = 0.001) and a higher incidence of visceral recurrence compared with normal/underweight patients. In a multivariable model, BMI remained significantly associated with both OS and RFS for the entire cohort. The interactions between BMI and LABC subsets and between BMI and menopausal status were not statistically significant. CONCLUSION: Patients with LABC and high BMI have a worse prognosis. Evaluation of the biological factors associated with this observation can provide tools for additional therapeutic interventions.},
author = {Dawood, Shaheenah and Broglio, Kristine and Gonzalez-Angulo, Ana M and Kau, Shu-Wan and Islam, Rabiul and Hortobagyi, Gabriel N and Cristofanilli, Massimo},
doi = {10.1158/1078-0432.CCR-07-1479},
file = {:home/riku/Documents/Mendeley Desktop/Dawood et al/Dawood et al.{\_}2008{\_}Prognostic value of body mass index in locally advanced breast cancer.pdf:pdf},
issn = {1078-0432},
journal = {Clin. Cancer Res.},
number = {6},
pages = {1718--1725},
pmid = {18347172},
title = {{Prognostic value of body mass index in locally advanced breast cancer.}},
volume = {14},
year = {2008}
}
@article{Løning2013,
abstract = {Following their successful implementation for the treatment of metastatic breast cancer, the 'third-generation' aromatase inhibitors (anastrozole, letrozole, and exemestane) have now become standard adjuvant endocrine treatment for postmenopausal estrogen receptor-positive breast cancers. These drugs are characterized by potent aromatase inhibition, causing {\textgreater}98{\%} inhibition of estrogen synthesis in vivo. A recent meta-analysis found no difference in anti-tumor efficacy between these three compounds. As of today, aromatase inhibitor monotherapy and sequential treatment using tamoxifen followed by an aromatase inhibitor for a total of 5 years are considered equipotent treatment options. However, current trials are addressing the potential benefit of extending treatment duration beyond 5 years. Regarding side effects, aromatase inhibitors are not found associated with enhanced risk of cardiovascular disease, and enhanced bone loss is prevented by adding bisphosphonates in concert for those at danger of developing osteoporosis. However, arthralgia and carpal tunnel syndrome preclude drug administration among a few patients. While recent findings have questioned the use of aromatase inhibitors among overweight and, in particular, obese patients, this problem seems to focus on premenopausal patients treated with an aromatase inhibitor and an LH-RH analog in concert, questioning the efficacy of LH-RH analogs rather than aromatase inhibitors among overweight patients. Finally, recent findings revealing a benefit from adding the mTOR inhibitor everolimus to endocrine treatment indicate targeted therapy against defined growth factor pathways to be a way forward, by reversing acquired resistance to endocrine therapy.},
author = {L{\o}ning, Per Eystein and Eikesdal, Hans Petter},
doi = {10.1530/ERC-13-0099},
file = {:home/riku/Documents/Mendeley Desktop/L{\o}ning, Eikesdal/L{\o}ning, Eikesdal{\_}2013{\_}Aromatase inhibition 2013 Clinical state of the art and questions that remain to be solved.pdf:pdf},
isbn = {1479-6821 (Electronic)$\backslash$n1351-0088 (Linking)},
issn = {13510088},
journal = {Endocr. Relat. Cancer},
keywords = {Adjuvant therapy,Aromatase inhibitors,Breast cancer,Endocrine therapy,Resistance},
pmid = {23625614},
title = {{Aromatase inhibition 2013: Clinical state of the art and questions that remain to be solved}},
volume = {20},
year = {2013}
}
@article{Leek2012,
abstract = {Heterogeneity and latent variables are now widely recognized as major sources of bias and variability in high-throughput experiments. The most well-known source of latent variation in genomic experiments are batch effects-when samples are processed on different days, in different groups or by different people. However, there are also a large number of other variables that may have a major impact on high-throughput measurements. Here we describe the sva package for identifying, estimating and removing unwanted sources of variation in high-throughput experiments. The sva package supports surrogate variable estimation with the sva function, direct adjustment for known batch effects with the ComBat function and adjustment for batch and latent variables in prediction problems with the fsva function.},
author = {Leek, Jeffrey T. and Johnson, W. Evan and Parker, Hilary S. and Jaffe, Andrew E. and Storey, John D.},
doi = {10.1093/bioinformatics/bts034},
file = {:home/riku/Documents/Mendeley Desktop/Leek et al/Leek et al.{\_}2012{\_}The SVA package for removing batch effects and other unwanted variation in high-throughput experiments.pdf:pdf},
isbn = {1367480314602059},
issn = {13674803},
journal = {Bioinformatics},
number = {6},
pages = {882--883},
pmid = {22257669},
title = {{The SVA package for removing batch effects and other unwanted variation in high-throughput experiments}},
volume = {28},
year = {2012}
}
@article{Holder2000,
abstract = {Studies of mice and humans have revealed a number of genes that when mutated result in severe obesity. We have studied a unique girl with early-onset obesity and a de novo balanced translocation between chromosomes 1p22.1 and 6q16.2. Her weight gain is most likely due to excessive food intake, since measured energy expenditure was normal. We cloned and sequenced both translocation breakpoints. The translocation does not appear to affect any transcription unit on 1p, but it disrupts the SIM1 gene on 6q. SIM1 encodes a human homolog of Drosophila Sim (Single-minded), a transcription factor involved in midline neurogenesis, and is a prototypical member of the bHLH-PAS (basic helix-loop-helix + period, aryl hydrocarbon receptor, Single-minded) gene family. Our subject's trans- location separates the 5' promoter region and bHLH domain from the 3' PAS and putative transcriptional regulation domains. The transcriptional targets of SIM1 are not known. Mouse Sim1 is expressed in the developing kidney and central nervous system, and is essential for formation of the supraoptic and paraventricular (PVN) nuclei of the hypothalamus. Previous neuroanatomical and pharmacological studies have implicated the PVN in the regulation of body weight: PVN neurons express the melanocortin 4 receptor and appear to be physiological targets of alpha-melanocyte-stimulating hormone, which inhibits food intake. We hypothesize that haploinsufficiency of SIM1, possibly acting upstream or downstream of the melanocortin 4 receptor in the PVN, is responsible for severe obesity in our subject.},
author = {Holder, J L and Butte, N F and Zinn, a R},
doi = {ddd012 [pii]},
file = {:home/riku/Documents/Mendeley Desktop/Holder, Butte, Zinn/Holder, Butte, Zinn{\_}2000{\_}Profound obesity associated with a balanced translocation that disrupts the SIM1 gene.pdf:pdf},
isbn = {0964-6906},
issn = {0964-6906},
journal = {Hum. Mol. Genet.},
keywords = {obesity},
mendeley-tags = {obesity},
number = {1},
pages = {101--108},
pmid = {10587584},
title = {{Profound obesity associated with a balanced translocation that disrupts the SIM1 gene.}},
volume = {9},
year = {2000}
}
@article{Albuquerque2015,
abstract = {It is well-known that obesity is a complex multifactorial and heterogeneous condition with an important genetic component. Recently, major advances in obesity research emerged concerning the molecular mechanisms contributing to the obese condition. This review outlines several studies and data concerning the genetics and other important factors in the susceptibility risk to develop obesity. Based in the genetic etiology three main categories of obesity are considered: monogenic, syndromic, and common obesity. For the monogenic forms of obesity, the gene causing the phenotype is clearly identified, whereas for the common obesity the loci architecture underlying the phenotype is still being characterized. Given that, in this review we focus mainly in this obesity form, reviewing loci found until now by genome-wide association studies related with the susceptibility risk to develop obesity. Moreover, we also detail the obesity-related loci identified in children and in different ethnic groups, trying to highlight the complexity of the genetics underlying the common obese phenotype. Importantly, we also focus in the evolutionary hypotheses that have been proposed trying to explain how natural selection favored the spread of genes that increase the risk for an obese phenotype and how this predisposition to obesity evolved. Other factors are important in the obesity condition, and thus, we also discuss the epigenetic mechanisms involved in the susceptibility and development of obesity. Covering all these topics we expect to provide a complete and recent perspective about the underlying mechanisms involved in the development and origin of obesity. Only with a full understanding of the factors and mechanisms contributing to obesity, it will be possible to provide and allow the development of new therapeutic approaches to this condition.},
author = {Albuquerque, David and Stice, Eric and Rodr{\'{i}}guez-L{\'{o}}pez, Raquel and Manco, Lic{\'{i}}no and N{\'{o}}brega, Cl{\'{e}}vio},
doi = {10.1007/s00438-015-1015-9},
file = {:home/riku/Documents/Mendeley Desktop/Albuquerque et al/Albuquerque et al.{\_}2015{\_}Current review of genetics of human obesity from molecular mechanisms to an evolutionary perspective.pdf:pdf},
isbn = {1617-4615},
issn = {16174623},
journal = {Mol. Genet. Genomics},
keywords = {Epigenetics,Evolutionary perspectives,Genetics of obesity,MicroRNAs,Nutrigenomics,Obesity,obesity},
mendeley-tags = {obesity},
pages = {1191--1221},
pmid = {25749980},
publisher = {Springer Berlin Heidelberg},
title = {{Current review of genetics of human obesity: from molecular mechanisms to an evolutionary perspective}},
volume = {290},
year = {2015}
}
@article{Smyth2004,
abstract = {The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential expression in a replicated two-color experiment using a simple hierarchical parametric model. The purpose of this paper is to develop the hierarchical model of Lonnstedt and Speed (2002) into a practical approach for general microarray experiments with arbitrary numbers of treatments and RNA samples. The model is reset in the context of general linear models with arbitrary coefficients and contrasts of interest. The approach applies equally well to both single channel and two color microarray experiments. Consistent, closed form estimators are derived for the hyperparameters in the model. The estimators proposed have robust behavior even for small numbers of arrays and allow for incomplete data arising from spot filtering or spot quality weights. The posterior odds statistic is reformulated in terms of a moderated t-statistic in which posterior residual standard deviations are used in place of ordinary standard deviations. The empirical Bayes approach is equivalent to shrinkage of the estimated sample variances towards a pooled estimate, resulting in far more stable inference when the number of arrays is small. The use of moderated t-statistics has the advantage over the posterior odds that the number of hyperparameters which need to estimated is reduced; in particular, knowledge of the non-null prior for the fold changes are not required. The moderated t-statistic is shown to follow a t-distribution with augmented degrees of freedom. The moderated t inferential approach extends to accommodate tests of composite null hypotheses through the use of moderated F-statistics. The performance of the methods is demonstrated in a simulation study. Results are presented for two publicly available data sets.},
author = {Smyth, Gordon K},
doi = {10.2202/1544-6115.1027},
file = {:home/riku/Documents/Mendeley Desktop/Smyth/Smyth{\_}2004{\_}Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments Linear Models and E.pdf:pdf},
isbn = {1544-6115; 1544-6115},
issn = {1544-6115},
journal = {Stat. Appl. Genet. Mol. Biol.},
number = {1},
pages = {1--26},
pmid = {16646809},
title = {{Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments}},
volume = {3},
year = {2004}
}
@article{Wu2012,
abstract = {Competitive gene set tests are commonly used in molecular pathway analysis to test for enrichment of a particular gene annotation category amongst the differential expression results from a microarray experiment. Existing gene set tests that rely on gene permutation are shown here to be extremely sensitive to inter-gene correlation. Several data sets are analyzed to show that inter-gene correlation is non-ignorable even for experiments on homogeneous cell populations using genetically identical model organisms. A new gene set test procedure (CAMERA) is proposed based on the idea of estimating the inter-gene correlation from the data, and using it to adjust the gene set test statistic. An efficient procedure is developed for estimating the inter-gene correlation and characterizing its precision. CAMERA is shown to control the type I error rate correctly regardless of inter-gene correlations, yet retains excellent power for detecting genuine differential expression. Analysis of breast cancer data shows that CAMERA recovers known relationships between tumor subtypes in very convincing terms. CAMERA can be used to analyze specified sets or as a pathway analysis tool using a database of molecular signatures.},
author = {Wu, Di and Smyth, Gordon K.},
doi = {10.1093/nar/gks461},
file = {:home/riku/Documents/Mendeley Desktop/Wu, Smyth/Wu, Smyth{\_}2012{\_}Camera A competitive gene set test accounting for inter-gene correlation.pdf:pdf},
isbn = {1362-4962 (Electronic) 0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {17},
pages = {e133},
pmid = {22638577},
title = {{Camera: A competitive gene set test accounting for inter-gene correlation}},
volume = {40},
year = {2012}
}
@article{Fuentes-Mattei2014,
abstract = {BACKGROUND: Obesity increases the risk of cancer death among postmenopausal women with estrogen receptor-positive (ER+) breast cancer, but the direct evidence for the mechanisms is lacking. The purpose of this study is to demonstrate direct evidence for the mechanisms mediating this epidemiologic phenomenon. METHODS: We analyzed transcriptomic profiles of pretreatment biopsies from a prospective cohort of 137 ER+ breast cancer patients. We generated transgenic (MMTV-TGF$\alpha$;A (y) /a) and orthotopic/syngeneic (A (y) /a) obese mouse models to investigate the effect of obesity on tumorigenesis and tumor progression and to determine biological mechanisms using whole-genome transcriptome microarrays and protein analyses. We used a coculture system to examine the impact of adipocytes/adipokines on breast cancer cell proliferation. All statistical tests were two-sided. RESULTS: Functional transcriptomic analysis of patients revealed the association of obesity with 59 biological functional changes (P {\textless} .05) linked to cancer hallmarks. Gene enrichment analysis revealed enrichment of AKT-target genes (P = .04) and epithelial-mesenchymal transition genes (P = .03) in patients. Our obese mouse models demonstrated activation of the AKT/mTOR pathway in obesity-accelerated mammary tumor growth (3.7- to 7.0-fold; P {\textless} .001; n = 6-7 mice per group). Metformin or everolimus can suppress obesity-induced secretion of adipokines and breast tumor formation and growth (0.5-fold, P = .04; 0.3-fold, P {\textless} .001, respectively; n = 6-8 mice per group). The coculture model revealed that adipocyte-secreted adipokines (eg, TIMP-1) regulate adipocyte-induced breast cancer cell proliferation and invasion. Metformin suppress adipocyte-induced cell proliferation and adipocyte-secreted adipokines in vitro. CONCLUSIONS: Adipokine secretion and AKT/mTOR activation play important roles in obesity-accelerated breast cancer aggressiveness in addition to hyperinsulinemia, estrogen signaling, and inflammation. Metformin and everolimus have potential for therapeutic interventions of ER+ breast cancer patients with obesity.},
author = {Fuentes-Mattei, Enrique and Velazquez-Torres, Guermarie and Phan, Liem and Zhang, F. and Chou, P.-C. and Shin, J.-H. and Choi, Hyun Ho and Chen, J.-S. and Zhao, Ruiying and Chen, Jian and Gully, Chris and Carlock, Colin and Qi, Yuan and Zhang, Ya and Wu, Yun and Esteva, Francisco J. and Luo, Yongde and McKeehan, Wallace L. and Ensor, Joe and Hortobagyi, Gabriel N. and Pusztai, Lajos and {Fraser Symmans}, W. and Lee, M.-H. and {Jim Yeung}, S.-C.},
doi = {10.1093/jnci/dju158},
file = {:home/riku/Documents/Mendeley Desktop/Fuentes-Mattei et al/Fuentes-Mattei et al.{\_}2014{\_}Effects of Obesity on Transcriptomic Changes and Cancer Hallmarks in Estrogen Receptor-Positive Breast Cancer.pdf:pdf},
issn = {0027-8874},
journal = {J. Natl. Cancer Inst.},
keywords = {Key Paper},
mendeley-tags = {Key Paper},
month = {jun},
number = {7},
pages = {dju158},
pmid = {24957076},
title = {{Effects of Obesity on Transcriptomic Changes and Cancer Hallmarks in Estrogen Receptor-Positive Breast Cancer}},
volume = {106},
year = {2014}
}
@article{Yap2012,
abstract = {Most advanced solid tumors remain incurable, with resistance to chemotherapeutics and targeted therapies a common cause of poor clinical outcome. Intratumor heterogeneity may contribute to this failure by initiating phenotypic diversity enabling drug resistance to emerge and by introducing tumor sampling bias. Envisaging tumor growth as a Darwinian tree with the trunk representing ubiquitous mutations and the branches representing heterogeneous mutations may help in drug discovery and the development of predictive biomarkers of drug response.},
author = {Yap, T. A. and Gerlinger, M. and Futreal, P. A. and Pusztai, L. and Swanton, C.},
doi = {10.1126/scitranslmed.3003854},
file = {:home/riku/Documents/Mendeley Desktop/Yap et al/Yap et al.{\_}2012{\_}Intratumor Heterogeneity Seeing the Wood for the Trees(2).pdf:pdf},
isbn = {1946-6242 (Electronic)$\backslash$n1946-6234 (Linking)},
issn = {1946-6234},
journal = {Sci. Transl. Med.},
number = {127},
pages = {127ps10--127ps10},
pmid = {22461637},
title = {{Intratumor Heterogeneity: Seeing the Wood for the Trees}},
volume = {4},
year = {2012}
}
@article{Swinburn2011,
abstract = {The simultaneous increases in obesity in almost all countries seem to be driven mainly by changes in the global food system, which is producing more processed, affordable, and effectively marketed food than ever before. This passive overconsumption of energy leading to obesity is a predictable outcome of market economies predicated on consumption-based growth. The global food system drivers interact with local environmental factors to create a wide variation in obesity prevalence between populations. Within populations, the interactions between environmental and individual factors, including genetic makeup, explain variability in body size between individuals. However, even with this individual variation, the epidemic has predictable patterns in subpopulations. In low-income countries, obesity mostly affects middle-aged adults (especially women) from wealthy, urban environments; whereas in high-income countries it affects both sexes and all ages, but is disproportionately greater in disadvantaged groups. Unlike other major causes of preventable death and disability, such as tobacco use, injuries, and infectious diseases, there are no exemplar populations in which the obesity epidemic has been reversed by public health measures. This absence increases the urgency for evidence-creating policy action, with a priority on reduction of the supply-side drivers. ?? 2011 Elsevier Ltd.},
author = {Swinburn, Boyd A. and Sacks, Gary and Hall, Kevin D. and McPherson, Klim and Finegood, Diane T. and Moodie, Marjory L. and Gortmaker, Steven L.},
doi = {10.1016/S0140-6736(11)60813-1},
file = {:home/riku/Documents/Mendeley Desktop/Swinburn et al/Swinburn et al.{\_}2011{\_}The global obesity pandemic Shaped by global drivers and local environments.pdf:pdf},
isbn = {01406736},
issn = {01406736},
journal = {Lancet},
keywords = {obesity},
mendeley-tags = {obesity},
number = {9793},
pages = {804--814},
pmid = {21872749},
title = {{The global obesity pandemic: Shaped by global drivers and local environments}},
volume = {378},
year = {2011}
}
@article{Langfelder2008,
author = {Langfelder, Peter and Horvath, Steve},
doi = {10.1186/1471-2105-9-559},
file = {:home/riku/Documents/Mendeley Desktop/Langfelder, Horvath/Langfelder, Horvath{\_}2008{\_}WGCNA an R package for weighted correlation network analysis.pdf:pdf},
journal = {BMC Bioinformatics},
pages = {559},
title = {{WGCNA : an R package for weighted correlation network analysis}},
volume = {9},
year = {2008}
}
@misc{R2016,
author = {{R Development Core Team}},
title = {{R: A language and environment for statictical computing}},
url = {https://www.r-project.org/},
urldate = {2016-01-09},
year = {2016}
}
@article{Bild2006,
abstract = {The development of an oncogenic state is a complex process involving the accumulation of multiple independent mutations that lead to deregulation of cell signalling pathways central to the control of cell growth and cell fate. The ability to define cancer subtypes, recurrence of disease and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies. Various studies have also demonstrated the potential for using gene expression profiles for the analysis of oncogenic pathways. Here we show that gene expression signatures can be identified that reflect the activation status of several oncogenic pathways. When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumours and clinically relevant associations with disease outcomes. Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumour subtypes. Clustering tumours based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers. Predictions of pathway deregulation in cancer cell lines are also shown to predict the sensitivity to therapeutic agents that target components of the pathway. Linking pathway deregulation with sensitivity to therapeutics that target components of the pathway provides an opportunity to make use of these oncogenic pathway signatures to guide the use of targeted therapeutics.},
author = {Bild, Andrea H and Yao, Guang and Chang, Jeffrey T and Wang, Quanli and Potti, Anil and Chasse, Dawn and Joshi, Mary-Beth and Harpole, David and Lancaster, Johnathan M and Berchuck, Andrew and Olson, John a and Marks, Jeffrey R and Dressman, Holly K and West, Mike and Nevins, Joseph R},
doi = {10.1038/nature04296},
file = {:home/riku/Documents/Mendeley Desktop/Bild et al/Bild et al.{\_}2006{\_}Oncogenic pathway signatures in human cancers as a guide to targeted therapies.pdf:pdf},
isbn = {1476-4687 (Electronic)},
issn = {0028-0836},
journal = {Nature},
number = {7074},
pages = {353--357},
pmid = {16273092},
title = {{Oncogenic pathway signatures in human cancers as a guide to targeted therapies.}},
volume = {439},
year = {2006}
}
@article{Bernstein1993,
abstract = {There is substantial evidence that high estrogen levels in postmenopausal women are associated with an increase in breast cancer risk, but such a relation has not yet been established in premenopausal women, despite biologic evidence that breast epithelial cell division rates are high during the luteal phase of the menstrual cycle when estradiol and progesterone levels are high. The lack of total consistency among studies that have assessed estrogen differences, whether in breast cancer patients versus controls or in subgroups of the population characterized by different risk profiles for breast cancer, is not unexpected given the extraordinarily complex methodological issues that must be addressed in these studies. There has been a clear evolution over time in the level of sophistication of these types of studies, further decreasing the likelihood of finding consistent patterns in the literature. Other hormones may play an important role in breast cancer development as well. Experimental data are particularly compelling for a role of progesterone and prolactin, but hormonal studies in women are not entirely convincing regarding the role of these two hormones, nor is the literature nearly as extensive as it is for the estrogens. Studies of various androgens are even less consistent. Moreover, such studies suffer from a lack of precise hypotheses regarding how these hormones might directly alter risk.},
author = {Bernstein, L and Ross, R K},
file = {:home/riku/Documents/Mendeley Desktop/Bernstein, Ross/Bernstein, Ross{\_}1993{\_}Endogenous hormones and breast cancer risk.pdf:pdf},
isbn = {0193-936X (Print)$\backslash$r0193-936X (Linking)},
issn = {0193-936X},
journal = {Epidemiol. Rev.},
number = {1},
pages = {48--65},
pmid = {8405212},
title = {{Endogenous hormones and breast cancer risk.}},
volume = {15},
year = {1993}
}
@article{Ofei2005,
abstract = {Obesity is a common and preventable disease of clinical and public health importance. It is often a major risk factor for the development of several non-communicable diseases, significant disability and premature death. There is presently a global epidemic of obesity in all age groups and in both developed and developing countries. The increasing prevalence of obesity places a large burden on health care use and costs. Weight loss is associated with significant health and economic benefits. Effective weight loss strategies include dietary therapy, physical activity and lifestyle modification. Drug therapy is reserved for obese or overweight patients who have concomitant obesity-related risk factors or diseases. Population-wide prevention programmes have a greater potential of stemming the obesity epidemic and being more cost-effective than clinic-based weight-loss programmes. Ghana is going through an economic and nutrition transition and experiencing an increase in the prevalence of obesity and obesity-related illnesses, especially among women and urban dwellers. A national taskforce to address this epidemic and to draw up a national policy on related non-communicable diseases is urgently needed.},
author = {Ofei, F},
doi = {10.1182/blood-2005-07-2977},
file = {:home/riku/Documents/Mendeley Desktop/Ofei/Ofei{\_}2005{\_}Obesity - a preventable disease.pdf:pdf},
isbn = {0016-9560 (Print)$\backslash$r0016-9560 (Linking)},
issn = {0016-9560},
journal = {Ghana Med. J.},
keywords = {ab-,around the waist and,cardiovascular disease,hypertension,mellitus,non-communicable disease,obesity,overweight,the body - either,trunk,type 2 diabetes},
mendeley-tags = {obesity},
number = {3},
pages = {98--101},
pmid = {17299552},
title = {{Obesity - a preventable disease.}},
volume = {39},
year = {2005}
}
@article{Alter2000,
abstract = {We describe the use of singular value decomposition in transforming genome-wide expression data from genes x arrays space to reduced diagonalized "eigengenes" x "eigenarrays" space, where the eigengenes (or eigenarrays) are unique orthonormal superpositions of the genes (or arrays). Normalizing the data by filtering out the eigengenes (and eigenarrays) that are inferred to represent noise or experimental artifacts enables meaningful comparison of the expression of different genes across different arrays in different experiments. Sorting the data according to the eigengenes and eigenarrays gives a global picture of the dynamics of gene expression, in which individual genes and arrays appear to be classified into groups of similar regulation and function, or similar cellular state and biological phenotype, respectively. After normalization and sorting, the significant eigengenes and eigenarrays can be associated with observed genome-wide effects of regulators, or with measured samples, in which these regulators are overactive or underactive, respectively.},
author = {Alter, O. and Brown, P. O. and Botstein, D.},
doi = {10.1073/pnas.97.18.10101},
file = {:home/riku/Documents/Mendeley Desktop/Alter, Brown, Botstein/Alter, Brown, Botstein{\_}2000{\_}Singular value decomposition for genome-wide expression data processing and modeling.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
keywords = {Biological,Cell Cycle,Fungal,Genetic,Genome,Mathematics,Models,Oligonucleotide Array Sequence Analysis,Open Reading Frames,Saccharomyces cerevisiae,Saccharomyces cerevisiae: cytology,Saccharomyces cerevisiae: genetics,Statistical},
number = {18},
pages = {10101--10106},
pmid = {10963673},
title = {{Singular value decomposition for genome-wide expression data processing and modeling}},
volume = {97},
year = {2000}
}
@article{Creighton2012,
abstract = {Obesity is thought to contribute to worse disease outcome in breast cancer as a result of increased levels of adipocyte-secreted endocrine factors, insulin, and insulin-like growth factors (IGFs) that accelerate tumor cell proliferation and impair treatment response. We examined the effects of patient obesity on primary breast tumor gene expression, by profiling transcription of a set of 103 tumors for which the patients' body mass index (BMI) was ascertained. Sample profiles were stratified according to patients' obesity phenotype defined as normal (BMI {\textless} 25), overweight (BMI 25-29.9), or obese (BMI ≥ 30). Widespread gene expression alterations were evident in breast tumors from obese patients as compared to other tumors, allowing us to define an obesity-associated cancer transcriptional signature of 662 genes. In multiple public expression data sets of breast cancers (representing {\textgreater} 1,500 patients), manifestation of the obesity signature patterns correlated with manifestation of a gene signature for IGF signaling and (to a lesser extent) with lower levels of estrogen receptor. In one patient cohort, manifestation of the obesity signature correlated with shorter time to metastases. A number of small molecules either induced or suppressed the obesity-associated transcriptional program in vitro; estrogens alpha-estradiol, levonorgestrel, and hexestrol induced the program, while several anti-parkinsonian agents targeting neurotransmitter receptor pathways repressed the program. Obesity in breast cancer patients appears to impact the gene expression patterns of the tumor (perhaps as a result of altered body chemistry). These results warrant further investigation of obesity-associated modifiers of breast cancer risk and disease outcome.},
author = {Creighton, Chad J. and Sada, Yvonne H. and Zhang, Yiqun and Tsimelzon, Anna and Wong, Helen and Dave, Bhuvanesh and Landis, Melissa D. and Bear, Harry D. and Rodriguez, Angel and Chang, Jenny C.},
doi = {10.1007/s10549-011-1595-y},
file = {:home/riku/Documents/Mendeley Desktop/Creighton et al/Creighton et al.{\_}2012{\_}A gene transcription signature of obesity in breast cancer.pdf:pdf},
isbn = {1573-7217 (Electronic) 0167-6806 (Linking)},
issn = {01676806},
journal = {Breast Cancer Res. Treat.},
keywords = {BMI,Breast cancer,Gene expression profiling,IGF,Insulin-like growth factor,Key Paper,Obesity},
mendeley-tags = {Key Paper},
pages = {993--1000},
pmid = {21750966},
title = {{A gene transcription signature of obesity in breast cancer}},
volume = {132},
year = {2012}
}
@article{Moustafa2013,
abstract = {Obesity is a disorder characterized by an excess accumulation of body fat resulting from a mismatch between energy intake and expenditure. Incidence of obesity has increased dramatically in the past few years, almost certainly fuelled by a shift in dietary habits owing to the widespread availability of low-cost, hypercaloric foods. However, clear differences exist in obesity susceptibility among individuals exposed to the same obesogenic environment, implicating genetic risk factors. Numerous genes have been shown to be involved in the development of monofactorial forms of obesity. In genome-wide association studies, a large number of common variants have been associated with adiposity levels, each accounting for only a small proportion of the predicted heritability. Although the small effect sizes of obesity variants identified in genome-wide association studies currently preclude their utility in clinical settings, screening for a number of monogenic obesity variants is now possible. Such regular screening will provide more informed prognoses and help in the identification of at-risk individuals who could benefit from early intervention, in evaluation of the outcomes of current obesity treatments, and in personalization of the clinical management of obesity. This Review summarizes current advances in obesity genetics and discusses the future of research in this field and the potential relevance to personalized obesity therapy.},
author = {{El-Sayed Moustafa}, Julia S and Froguel, Philippe},
doi = {10.1038/nrendo.2013.57},
file = {:home/riku/Documents/Mendeley Desktop/El-Sayed Moustafa, Froguel/El-Sayed Moustafa, Froguel{\_}2013{\_}From obesity genetics to the future of personalized obesity therapy.pdf:pdf},
isbn = {1759-5037 (Electronic)$\backslash$r1759-5029 (Linking)},
issn = {1759-5037},
journal = {Nat. Rev. Endocrinol.},
keywords = {Animals,Body Mass Index,Genetic Predisposition to Disease,Genetic Predisposition to Disease: genetics,Humans,Obesity,Obesity: diagnosis,Obesity: genetics,obesity},
mendeley-tags = {obesity},
number = {7},
pages = {402--13},
pmid = {23529041},
publisher = {Nature Publishing Group},
title = {{From obesity genetics to the future of personalized obesity therapy.}},
volume = {9},
year = {2013}
}
@article{Schena1995,
abstract = {A high-capacity system was developed to monitor the expression of many genes in parallel. Microarrays prepared by high-speed robotic printing of complementary DNAs on glass were used for quantitative expression measurements of the corresponding genes. Because of the small format and high density of the arrays, hybridization volumes of 2 microliters could be used that enabled detection of rare transcripts in probe mixtures derived from 2 micrograms of total cellular messenger RNA. Differential expression measurements of 45 Arabidopsis genes were made by means of simultaneous, two-color fluorescence hybridization.},
author = {Schena, Mark and Shalon, Dari and Davis, Ronald W. and Brown, Patrick O.},
doi = {10.1126/science.270.5235.467},
file = {:home/riku/Documents/Mendeley Desktop/Schena et al/Schena et al.{\_}1995{\_}Quantitative monitoring of gene expression patterns with a complementary DNA microarray.pdf:pdf},
isbn = {0036-8075},
issn = {0036-8075},
journal = {Science (80-. ).},
number = {5235},
pages = {467--470},
pmid = {7569999},
title = {{Quantitative monitoring of gene expression patterns with a complementary DNA microarray}},
volume = {270},
year = {1995}
}
@article{Gatza2010a,
abstract = {The hallmark of human cancer is heterogeneity, reflecting the complexity and variability of the vast array of somatic mutations acquired during oncogenesis. An ability to dissect this heterogeneity, to identify subgroups that represent common mechanisms of disease, will be critical to understanding the complexities of genetic alterations and to provide a framework to develop rational therapeutic strategies. Here, we describe a classification scheme for human breast cancer making use of patterns of pathway activity to build on previous subtype characterizations using intrinsic gene expression signatures, to provide a functional interpretation of the gene expression data that can be linked to therapeutic options. We show that the identified subgroups provide a robust mechanism for classifying independent samples, identifying tumors that share patterns of pathway activity and exhibit similar clinical and biological properties, including distinct patterns of chromosomal alterations that were not evident in the heterogeneous total population of tumors. We propose that this classification scheme provides a basis for understanding the complex mechanisms of oncogenesis that give rise to these tumors and to identify rational opportunities for combination therapies.},
author = {Gatza, Michael L and Lucas, Joseph E and Barry, William T and Kim, Jong Wook and Wang, Quanli and Crawford, Matthew D and Datto, Michael B and Kelley, Michael and Mathey-Prevot, Bernard and Potti, Anil and Nevins, Joseph R},
doi = {10.1073/pnas.0912708107},
file = {:home/riku/Documents/Mendeley Desktop/Gatza et al/Gatza et al.{\_}2010{\_}A pathway-based classification of human breast cancer.pdf:pdf},
isbn = {0912708107},
issn = {1091-6490},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
keywords = {Key Paper},
mendeley-tags = {Key Paper},
number = {15},
pages = {6994--6999},
pmid = {20335537},
title = {{A pathway-based classification of human breast cancer.}},
volume = {107},
year = {2010}
}
@article{Golub1970,
abstract = {The matrix U consists of n orthonormalized eigenvectors associated with the n largest eigenvalues of AA r, and the matrix V consists of the orthonormalized eigenvectors of AZ A. The diagonal elements of 27 are the non-negative square roots of the eigenvalues of ATA; they are ...},
author = {Golub, G. H. and Reinsch, C.},
doi = {10.1007/BF02163027},
file = {:home/riku/Documents/Mendeley Desktop/Golub, Reinsch/Golub, Reinsch{\_}1970{\_}Singular value decomposition and least squares solutions.pdf:pdf},
isbn = {0029-599X},
issn = {0029599X},
journal = {Numer. Math.},
number = {5},
pages = {403--420},
title = {{Singular value decomposition and least squares solutions}},
volume = {14},
year = {1970}
}
@article{Gerken2007,
abstract = {Variants in the FTO (fat mass and obesity associated) gene are associated with increased body mass index in humans. Here, we show by bioinformatics analysis that FTO shares sequence motifs with Fe(II)- and 2-oxoglutarate-dependent oxygenases. We find that recombinant murine Fto catalyzes the Fe(II)- and 2OG-dependent demethylation of 3-methylthymine in single-stranded DNA, with concomitant production of succinate, formaldehyde, and carbon dioxide. Consistent with a potential role in nucleic acid demethylation, Fto localizes to the nucleus in transfected cells. Studies of wild-type mice indicate that Fto messenger RNA (mRNA) is most abundant in the brain, particularly in hypothalamic nuclei governing energy balance, and that Fto mRNA levels in the arcuate nucleus are regulated by feeding and fasting. Studies can now be directed toward determining the physiologically relevant FTO substrate and how nucleic acid methylation status is linked to increased fat mass.},
author = {Gerken, Thomas and Girard, Christophe A and Tung, Yi-Chun Loraine and Webby, Celia J and Saudek, Vladimir and Hewitson, Kirsty S and Yeo, Giles S H and McDonough, Michael A and Cunliffe, Sharon and McNeill, Luke A and Galvanovskis, Juris and Rorsman, Patrik and Robins, Peter and Prieur, Xavier and Coll, Anthony P and Ma, Marcella and Jovanovic, Zorica and Farooqi, I Sadaf and Sedgwick, Barbara and Barroso, In{\^{e}}s and Lindahl, Tomas and Ponting, Chris P and Ashcroft, Frances M and O'Rahilly, Stephen and Schofield, Christopher J},
doi = {10.1126/science.1151710},
file = {:home/riku/Documents/Mendeley Desktop/Gerken et al/Gerken et al.{\_}2007{\_}The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase.pdf:pdf},
isbn = {1095-9203 (Electronic)},
issn = {1095-9203},
journal = {Science (80-. ).},
keywords = {FTO,GWAS,obesity},
mendeley-tags = {FTO,GWAS,obesity},
number = {5855},
pages = {1469--1472},
pmid = {17991826},
title = {{The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase.}},
volume = {318},
year = {2007}
}
@article{Lawrence2014,
abstract = {Although a few cancer genes are mutated in a high proportion of tumours of a given type ({\textgreater}20{\%}), most are mutated at intermediate frequencies (2-20{\%}). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600-5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics.},
author = {Lawrence, Michael S and Stojanov, Petar and Mermel, Craig H and Robinson, James T and Garraway, Levi A and Golub, Todd R and Meyerson, Matthew and Gabriel, Stacey B and Lander, Eric S and Getz, Gad},
doi = {10.1038/nature12912},
file = {:home/riku/Documents/Mendeley Desktop/Lawrence et al/Lawrence et al.{\_}2014{\_}Discovery and saturation analysis of cancer genes across 21 tumour types.pdf:pdf},
isbn = {1476-4687 (Electronic)$\backslash$r0028-0836 (Linking)},
issn = {1476-4687},
journal = {Nature},
keywords = {Apoptosis,Apoptosis: genetics,Case-Control Studies,Cell Proliferation,Chromatin,Chromatin: genetics,DNA Mutational Analysis,Exome,Exome: genetics,Genes,Genome,Genomic Instability,Genomic Instability: genetics,Genomics,Human,Human: genetics,Humans,Immune Evasion,Immune Evasion: genetics,Mutation Rate,Neoplasm,Neoplasm: genetics,Neoplasms,Neoplasms: classification,Neoplasms: genetics,Neoplasms: pathology,Point Mutation,Point Mutation: genetics,Post-Transcriptional,Post-Transcriptional: genetics,RNA Processing,Sample Size},
number = {7484},
pages = {495--501},
pmid = {24390350},
publisher = {Nature Publishing Group},
title = {{Discovery and saturation analysis of cancer genes across 21 tumour types.}},
volume = {505},
year = {2014}
}
@article{Soon2011,
abstract = {Secretory factors that drive cancer progression are attractive immunotherapeutic targets. We used a whole-genome data-mining approach on multiple cohorts of breast tumours annotated for clinical outcomes to discover such factors. We identified Serine protease inhibitor Kazal-type 1 (SPINK1) to be associated with poor survival in estrogen receptor-positive (ER+) cases. Immunohistochemistry showed that SPINK1 was absent in normal breast, present in early and advanced tumours, and its expression correlated with poor survival in ER+ tumours. In ER- cases, the prognostic effect did not reach statistical significance. Forced expression and/or exposure to recombinant SPINK1 induced invasiveness without affecting cell proliferation. However, down-regulation of SPINK1 resulted in cell death. Further, SPINK1 overexpressing cells were resistant to drug-induced apoptosis due to reduced caspase-3 levels and high expression of Bcl2 and phospho-Bcl2 proteins. Intriguingly, these anti-apoptotic effects of SPINK1 were abrogated by mutations of its protease inhibition domain. Thus, SPINK1 affects multiple aggressive properties in breast cancer: survival, invasiveness and chemoresistance. Because SPINK1 effects are abrogated by neutralizing antibodies, we suggest that SPINK1 is a viable potential therapeutic target in breast cancer.},
author = {Soon, Wendy Weijia and Miller, Lance David and Black, Michael A. and Dalmasso, Cyril and Chan, Xiu Bin and Pang, Brendan and Ong, Chee Wee and Salto-Tellez, Manuel and Desai, Kartiki V. and Liu, Edison T.},
doi = {10.1002/emmm.201100150},
file = {:home/riku/Documents/Mendeley Desktop/Soon et al/Soon et al.{\_}2011{\_}Combined genomic and phenotype screening reveals secretory factor SPINK1 as an invasion and survival factor associated.pdf:pdf},
isbn = {1757-4684 (Electronic)$\backslash$r1757-4676 (Linking)},
issn = {17574676},
journal = {EMBO Mol. Med.},
keywords = {Breast cancer,Cancer therapy,Distant metastasis-free survival,Expression microarrays,Oncogenes},
pages = {451--464},
pmid = {21656687},
title = {{Combined genomic and phenotype screening reveals secretory factor SPINK1 as an invasion and survival factor associated with patient prognosis in breast cancer}},
volume = {3},
year = {2011}
}
@article{Gautier2004,
abstract = {MOTIVATION The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used. RESULTS The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we present the main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.},
author = {Gautier, Laurent and Cope, Leslie and Bolstad, Benjamin M. and Irizarry, Rafael A.},
doi = {10.1093/bioinformatics/btg405},
file = {:home/riku/Documents/Mendeley Desktop/Gautier et al/Gautier et al.{\_}2004{\_}Affy - Analysis of Affymetrix GeneChip data at the probe level.pdf:pdf},
isbn = {1367-4803 (Print)$\backslash$r1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {3},
pages = {307--315},
pmid = {14960456},
title = {{Affy - Analysis of Affymetrix GeneChip data at the probe level}},
volume = {20},
year = {2004}
}
@article{Johnson2007,
abstract = {Non-biological experimental variation or "batch effects" are commonly observed across multiple batches of microarray experiments, often rendering the task of combining data from these batches difficult. The ability to combine microarray data sets is advantageous to researchers to increase statistical power to detect biological phenomena from studies where logistical considerations restrict sample size or in studies that require the sequential hybridization of arrays. In general, it is inappropriate to combine data sets without adjusting for batch effects. Methods have been proposed to filter batch effects from data, but these are often complicated and require large batch sizes ( {\textgreater} 25) to implement. Because the majority of microarray studies are conducted using much smaller sample sizes, existing methods are not sufficient. We propose parametric and non-parametric empirical Bayes frameworks for adjusting data for batch effects that is robust to outliers in small sample sizes and performs comparable to existing methods for large samples. We illustrate our methods using two example data sets and show that our methods are justifiable, easy to apply, and useful in practice. Software for our method is freely available at: http://biosun1.harvard.edu/complab/batch/.},
author = {Johnson, W. Evan and Li, Cheng and Rabinovic, Ariel},
doi = {10.1093/biostatistics/kxj037},
file = {:home/riku/Documents/Mendeley Desktop/Johnson, Li, Rabinovic/Johnson, Li, Rabinovic{\_}2007{\_}Adjusting batch effects in microarray expression data using empirical Bayes methods.pdf:pdf},
isbn = {1465-4644, 1468-4357},
issn = {14654644},
journal = {Biostatistics},
keywords = {Batch effects,Empirical Bayes,Microarrays,Monte Carlo},
number = {1},
pages = {118--127},
pmid = {16632515},
title = {{Adjusting batch effects in microarray expression data using empirical Bayes methods}},
volume = {8},
year = {2007}
}
@article{Clement1998,
abstract = {The adipocyte-specific hormone leptin, the product of the obese (ob) gene, regulates adipose-tissue mass through hypothalamic effects on satiety and energy expenditure. Leptin acts through the leptin receptor, a single-transmembrane-domain receptor of the cytokine-receptor family. In rodents, homozygous mutations in genes encoding leptin or the leptin receptor cause early-onset morbid obesity, hyperphagia and reduced energy expenditure. These rodents also show hypercortisolaemia, alterations in glucose homeostasis, dyslipidaemia, and infertility due to hypogonadotropic hypogonadisms. In humans, leptin deficiency due to a mutation in the leptin gene is associated with early-onset obesity. Here we describe a homozygous mutation in the human leptin receptor gene that results in a truncated leptin receptor lacking both the transmembrane and the intracellular domains. In addition to their early-onset morbid obesity, patients homozygous for this mutation have no pubertal development and their secretion of growth hormone and thyrotropin is reduced. These results indicate that leptin is an important physiological regulator of several endocrine functions in humans.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Clement, K and Vaisse, C and Lahlou, N and Cabrol, S and Pelloux, V and Cassuto, D and Gourmelen, M and Dina, C and Chambaz, J and Lacorte, J M and Basdevant, A and Bougneres, P and Lebouc, Y and Froguel, P and Guy-Grand, B},
doi = {10.1038/32911},
eprint = {NIHMS150003},
file = {:home/riku/Documents/Mendeley Desktop/Clement et al/Clement et al.{\_}1998{\_}A mutation in the human leptin receptor gene causes obesity and pituitary dysfunction.pdf:pdf},
isbn = {0028-0836 (Print)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
keywords = {*Mutation,*Receptors, Cell Surface,Adult,Body Height,Body Weight,Carrier Proteins/*genetics/physiology,Cell Surface,Family Health,Female,Genotype,Homozygote,Human Growth Hormone/secretion,Humans,Leptin,Male,Messenger/metabolism,Obesity/*genetics,Pituitary Diseases/*genetics/physiopathology,Polymorphism, Single-Stranded Conformational,RNA, Messenger/metabolism,Receptors, Leptin,Single-Stranded Conformational,obesity},
mendeley-tags = {obesity},
number = {6674},
pages = {398--401},
pmid = {9537324},
title = {{A mutation in the human leptin receptor gene causes obesity and pituitary dysfunction}},
volume = {392},
year = {1998}
}
@article{VanHubbardS2000,
author = {{Van Hubbard S}},
file = {:home/riku/Documents/Mendeley Desktop/Van Hubbard S/Van Hubbard S{\_}2000{\_}Defining overweight and obesity what are the issues.pdf:pdf},
journal = {Am J Clin Nutr},
keywords = {obesity},
mendeley-tags = {obesity},
pages = {1067--8},
title = {{Defining overweight and obesity: what are the issues}},
volume = {72},
year = {2000}
}
@article{Schulze2001,
abstract = {Parallel quantification of large numbers of messenger RNA transcripts using microarray technology promises to provide detailed insight into cellular processes involved in the regulation of gene expression. This should allow new understanding of signalling networks that operate in the cell and of the molecular basis and classification of disease. But can the technology deliver such far-reaching promises?},
author = {Schulze, Almut and Downward, Julian},
doi = {10.1038/35087138},
file = {:home/riku/Documents/Mendeley Desktop/Schulze, Downward/Schulze, Downward{\_}2001{\_}Navigating gene expression using microarrays--a technology review.pdf:pdf},
isbn = {1465-7392},
issn = {1465-7392},
journal = {Nat. Cell Biol.},
number = {8},
pages = {E190--E195},
pmid = {11483980},
title = {{Navigating gene expression using microarrays--a technology review.}},
volume = {3},
year = {2001}
}
@article{Benjamini1995a,
author = {Benjamini, Yoav and Hochberg, Yosef},
file = {:home/riku/Documents/Mendeley Desktop/Benjamini, Hochberg/Benjamini, Hochberg{\_}1995{\_}Controlling the False Discovery Rate A Practical and Powerful Approach to Multiple Testing.pdf:pdf},
journal = {J. R. Stat. Soc. Ser. B},
number = {1},
pages = {289--300},
title = {{Controlling the False Discovery Rate : A Practical and Powerful Approach to Multiple Testing}},
volume = {57},
year = {1995}
}
@article{GO2000,
abstract = {Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.},
archivePrefix = {arXiv},
arxivId = {10614036},
author = {{Gene Ontology Consortium}},
doi = {10.1038/75556},
eprint = {10614036},
file = {:home/riku/Documents/Mendeley Desktop/Gene Ontology Consortium/Gene Ontology Consortium{\_}2000{\_}Gene Ontology Tool for The Unification of Biology.pdf:pdf},
isbn = {1061-4036 (Print)$\backslash$r1061-4036 (Linking)},
issn = {1061-4036},
journal = {Nat. Genet.},
number = {1},
pages = {25--29},
pmid = {10802651},
title = {{Gene Ontology: Tool for The Unification of Biology}},
volume = {25},
year = {2000}
}
@article{Lee2008,
abstract = {Objective: To determine which simple index of overweight and obesity is the best discriminator of cardiovascular risk factors. Study Design and Setting: This is a meta-analysis of published literature. MEDLINE was searched. Studies that used receiver-operating characteristics (ROC) curve analysis and published area under the ROC curves (AUC) for overweight and obesity indices with hypertension, type-2 diabetes, and/or dyslipidemia were included. The AUC for each of the four indices, with each risk factor, was pooled using a random-effects model; male and female data were analyzed separately. Results: Ten studies met the inclusion criteria. Body mass index (BMI) was the poorest discriminator for cardiovascular risk factors. Waist-to-height ratio (WHtR) was the best discriminator for hypertension, diabetes, and dyslipidemia in both sexes; its pooled AUC (95{\%} confidence intervals) ranged from 0.67 (0.64, 0.69) to 0.73 (0.70, 0.75) and from 0.68 (0.63, 0.72) to 0.76 (0.70, 0.81) in males and females, respectively. Conclusion: Statistical evidence supports the superiority of measures of centralized obesity, especially WHtR, over BMI, for detecting cardiovascular risk factors in both men and women. ?? 2008 Elsevier Inc. All rights reserved.},
author = {Lee, Crystal Man Ying and Huxley, Rachel R. and Wildman, Rachel P. and Woodward, Mark},
doi = {10.1016/j.jclinepi.2007.08.012},
file = {:home/riku/Documents/Mendeley Desktop/Lee et al/Lee et al.{\_}2008{\_}Indices of abdominal obesity are better discriminators of cardiovascular risk factors than BMI a meta-analysis.pdf:pdf},
isbn = {0895-4356},
issn = {08954356},
journal = {J. Clin. Epidemiol.},
keywords = {Body mass index,Cardiovascular risk factors,Meta-analysis,Obesity,ROC curve,Waist-to-height ratio,obesity},
mendeley-tags = {obesity},
number = {7},
pages = {646--653},
pmid = {18359190},
title = {{Indices of abdominal obesity are better discriminators of cardiovascular risk factors than BMI: a meta-analysis}},
volume = {61},
year = {2008}
}
@article{Malik2013,
abstract = {The worldwide increase in obesity and related chronic diseases has largely been driven by global trade liberalization, economic growth and rapid urbanization. These factors continue to fuel dramatic changes in living environments, diets and lifestyles in ways that promote positive energy balance. Nutritional transitions in low-income and middle-income countries are typically characterized by increases in the consumption of animal fat and protein, refined grains, and added sugar. This change is coupled with reductions in physical activity owing to more mechanized and technologically driven lifestyles. Given the high costs of obesity and comorbidities in terms of health-care expenditure and quality of life, prevention strategies are paramount, particularly in low-income and middle-income countries that must manage coexisting infectious diseases and undernutrition in addition to the obesity epidemic. As countries become increasingly urbanized, undernutrition and obesity can exist side by side within the same country, community or household, which is a particular challenge for health systems with limited resources. Owing to the scope and complexity of the obesity epidemic, prevention strategies and policies across multiple levels are needed in order to have a measurable effect. Changes should include high-level global policies from the international community and coordinated efforts by governments, organizations, communities and individuals to positively influence behavioural change.},
author = {Malik, Vasanti S and Willett, Walter C and Hu, Frank B},
doi = {10.1038/nrendo.2012.199},
file = {:home/riku/Documents/Mendeley Desktop/Malik, Willett, Hu/Malik, Willett, Hu{\_}2013{\_}Global obesity trends, risk factors and policy implications.pdf:pdf},
isbn = {1759-5029},
issn = {1759-5037},
journal = {Nat. Rev. Endocrinol.},
keywords = {Health Promotion,Humans,Life Style,Obesity,Obesity: epidemiology,Risk Factors,World Health,obesity},
mendeley-tags = {obesity},
number = {1},
pages = {13--27},
pmid = {23165161},
publisher = {Nature Publishing Group},
title = {{Global obesity: trends, risk factors and policy implications.}},
volume = {9},
year = {2013}
}
@article{Dina2007,
abstract = {We identified a set of SNPs in the first intron of the FTO (fat mass and obesity associated) gene on chromosome 16q12.2 that is consistently strongly associated with early-onset and severe obesity in both adults and children of European ancestry with an experiment-wise P value of 1.67 x 10(-26) in 2,900 affected individuals and 5,100 controls. The at-risk haplotype yields a proportion of attributable risk of 22{\%} for common obesity. We conclude that FTO contributes to human obesity and hence may be a target for subsequent functional analyses.},
author = {Dina, Christian and Meyre, David and Gallina, Sophie and Durand, Emmanuelle and K{\"{o}}rner, Antje and Jacobson, Peter and Carlsson, Lena M S and Kiess, Wieland and Vatin, Vincent and Lecoeur, Cecile and Delplanque, J{\'{e}}rome and Vaillant, Emmanuel and Pattou, Fran{\c{c}}ois and Ruiz, Juan and Weill, Jacques and Levy-Marchal, Claire and Horber, Fritz and Potoczna, Natascha and Hercberg, Serge and {Le Stunff}, Catherine and Bougn{\`{e}}res, Pierre and Kovacs, Peter and Marre, Michel and Balkau, Beverley and Cauchi, St{\'{e}}phane and Ch{\`{e}}vre, Jean-Claude and Froguel, Philippe},
doi = {10.1038/ng2048},
file = {:home/riku/Documents/Mendeley Desktop/Dina et al/Dina et al.{\_}2007{\_}Variation in FTO contributes to childhood obesity and severe adult obesity.pdf:pdf},
isbn = {1061-4036 (Print)$\backslash$n1061-4036 (Linking)},
issn = {1061-4036},
journal = {Nat. Genet.},
keywords = {Adiposity,Adult,Age of Onset,Body Composition,Body Mass Index,Case-Control Studies,Child,Chromosomes, Human, Pair 16,Chromosomes, Human, Pair 16: genetics,Cohort Studies,Europe,FTO,Female,GWAS,Genetic Predisposition to Disease,Genetic Variation,Genetic Variation: genetics,Human,Humans,Introns,Introns: genetics,Male,Middle Aged,Obesity,Obesity: genetics,Pair 16,Pair 16: genetics,Polymorphism, Single Nucleotide,Polymorphism, Single Nucleotide: genetics,Single Nucleotide,Single Nucleotide: genetics,obesity},
mendeley-tags = {FTO,GWAS,obesity},
number = {6},
pages = {724--726},
pmid = {17496892},
title = {{Variation in FTO contributes to childhood obesity and severe adult obesity.}},
volume = {39},
year = {2007}
}
@article{Lashinger2014,
author = {Lashinger, L M and Rossi, E L and Hursting, S D},
doi = {10.1038/clpt.2014.136},
file = {:home/riku/Documents/Mendeley Desktop/Lashinger, Rossi, Hursting/Lashinger, Rossi, Hursting{\_}2014{\_}Obesity and Resistance to Cancer Chemotherapy Interacting Roles of Inflammation and Metabolic Dysregulat.pdf:pdf},
issn = {0009-9236},
journal = {Clin. Pharmacol. Ther.},
number = {4},
pages = {458--463},
title = {{Obesity and Resistance to Cancer Chemotherapy: Interacting Roles of Inflammation and Metabolic Dysregulation}},
volume = {96},
year = {2014}
}
@article{Krude1998,
abstract = {Sequential cleavage of the precursor protein pre-pro-opiomelanocortin (POMC) generates the melanocortin peptides adrenocorticotrophin (ACTH), melanocyte-stimulating hormones (MSH) alpha, beta and gamma as well as the opioid-receptor ligand beta-endorphin. While a few cases of isolated ACTH deficiency have been reported (OMIM 201400), an inherited POMC defect has not been described so far. Recent studies in animal models elucidated a central role of alpha-MSH in the regulation of food intake by activation of the brain melanocortin-4-receptor (MC4-R; refs 3-5) and the linkage of human obesity to chromosome 2 in close proximity to the POMC locus, led to the proposal of an association of POMC with human obesity. The dual role of alpha-MSH in regulating food intake and influencing hair pigmentation predicts that the phenotype associated with a defect in POMC function would include obesity, alteration in pigmentation and ACTH deficiency. The observation of these symptoms in two probands prompted us to search for mutations within their POMC genes. Patient 1 was found to be a compound heterozygote for two mutations in exon 3 (G7013T, C7133delta) which interfere with appropriate synthesis of ACTH and alpha-MSH. Patient 2 was homozygous for a mutation in exon 2 (C3804A) which abolishes POMC translation. These findings represent the first examples of a genetic defect within the POMC gene and define a new monogenic endocrine disorder resulting in early-onset obesity, adrenal insufficiency and red hair pigmentation.},
author = {Krude, H and Biebermann, H and Luck, W and Horn, R and Brabant, G and Gr{\"{u}}ters, a},
doi = {10.1177/000992289903800416},
file = {:home/riku/Documents/Mendeley Desktop/Krude et al/Krude et al.{\_}1998{\_}Severe early-onset obesity, adrenal insufficiency and red hair pigmentation caused by POMC mutations in humans.pdf:pdf},
isbn = {1061-4036 (Print)$\backslash$r1061-4036 (Linking)},
issn = {0009-9228},
journal = {Nat. Genet.},
keywords = {obesity},
mendeley-tags = {obesity},
number = {2},
pages = {155--157},
pmid = {9620771},
title = {{Severe early-onset obesity, adrenal insufficiency and red hair pigmentation caused by POMC mutations in humans.}},
volume = {19},
year = {1998}
}
@article{Dixon2016,
abstract = {BACKGROUND Observational studies have reported a positive association between body mass index (BMI) and ovarian cancer risk. However, questions remain as to whether this represents a causal effect, or holds for all histological subtypes. The lack of association observed for serous cancers may, for instance, be due to disease-associated weight loss. Mendelian randomization (MR) uses genetic markers as proxies for risk factors to overcome limitations of observational studies. We used MR to elucidate the relationship between BMI and ovarian cancer, hypothesizing that genetically predicted BMI would be associated with increased risk of non-high grade serous ovarian cancers (non-HGSC) but not HGSC. METHODS We pooled data from 39 studies (14 047 cases, 23 003 controls) in the Ovarian Cancer Association Consortium. We constructed a weighted genetic risk score (GRS, partial F-statistic = 172), summing alleles at 87 single nucleotide polymorphisms previously associated with BMI, weighting by their published strength of association with BMI. Applying two-stage predictor-substitution MR, we used logistic regression to estimate study-specific odds ratios (OR) and 95{\%} confidence intervals (CI) for the association between genetically predicted BMI and risk, and pooled these using random-effects meta-analysis. RESULTS Higher genetically predicted BMI was associated with increased risk of non-HGSC (pooled OR = 1.29, 95{\%} CI 1.03-1.61 per 5 units BMI) but not HGSC (pooled OR = 1.06, 95{\%} CI 0.88-1.27). Secondary analyses stratified by behaviour/subtype suggested that, consistent with observational data, the association was strongest for low-grade/borderline serous cancers (OR = 1.93, 95{\%} CI 1.33-2.81). CONCLUSIONS Our data suggest that higher BMI increases risk of non-HGSC, but not the more common and aggressive HGSC subtype, confirming the observational evidence.},
author = {Dixon, Suzanne C and Nagle, Christina M and Thrift, Aaron P and Pharoah, Paul D P and Pearce, Celeste Leigh and Zheng, Wei and Painter, Jodie N and Chenevix-Trench, Aocs Group Australian Cancer Study Ovarian Cancer Georgia and Fasching, Peter A and Beckmann, Matthias W and Lambrechts, Diether and Vergote, Ignace and Lambrechts, Sandrina and {Van Nieuwenhuysen}, Els and Rossing, Mary Anne and Doherty, Jennifer A and Wicklund, Kristine G and Chang-Claude, Jenny and Rudolph, Anja and Moysich, Kirsten B and Odunsi, Kunle and Goodman, Marc T and Wilkens, Lynne R and Thompson, Pamela J and Shvetsov, Yurii B and D{\"{o}}rk, Thilo and Park-Simon, Tjoung-Won and Hillemanns, Peter and Bogdanova, Natalia and Butzow, Ralf and Nevanlinna, Heli and Pelttari, Liisa M and Leminen, Arto and Modugno, Francesmary and Ness, Roberta B and Edwards, Robert P and Kelley, Joseph L and Heitz, Florian and Karlan, Beth Y and Kj{\ae}r, Susanne K and H{\o}gdall, Estrid and Jensen, Allan and Goode, Ellen L and Fridley, Brooke L and Cunningham, Julie M and Winham, Stacey J and Giles, Graham G and Bruinsma, Fiona and Milne, Roger L and Southey, Melissa C and Hildebrandt, Michelle A T and Wu, Xifeng and Lu, Karen H and Liang, Dong and Levine, Douglas A and Bisogna, Maria and Schildkraut, Joellen M and Berchuck, Andrew and Cramer, Daniel W and Terry, Kathryn L and Bandera, Elisa V and Olson, Sara H and Salvesen, Helga B and Thomsen, Liv Cecilie and Kopperud, Reidun K and Bjorge, Line and Kiemeney, Lambertus A and Massuger, Leon F A G and Pejovic, Tanja and Cook, Linda S and Le, Nhu D and Swenerton, Kenneth D and Brooks-Wilson, Angela and Kelemen, Linda E and Lubi{\'{n}}ski, Jan and Huzarski, Tomasz and Gronwald, Jacek and Menkiszak, Janusz and Wentzensen, Nicolas and Brinton, Louise and Yang, Hannah and Lissowska, Jolanta and H{\o}gdall, Claus K and Lundvall, Lene and Song, Honglin and Tyrer, Jonathan P and Campbell, Ian and Eccles, Diana and Paul, James and Glasspool, Rosalind and Siddiqui, Nadeem and Whittemore, Alice S and Sieh, Weiva and McGuire, Valerie and Rothstein, Joseph H and Narod, Steven A and Phelan, Catherine and Risch, Harvey A and McLaughlin, John R and Anton-Culver, Hoda and Ziogas, Argyrios and Menon, Usha and Gayther, Simon A and Ramus, Susan J and Gentry-Maharaj, Aleksandra and Wu, Anna H and Pike, Malcolm C and Tseng, Chiu-Chen and Kupryjanczyk, Jolanta and Dansonka-Mieszkowska, Agnieszka and Budzilowska, Agnieszka and Spiewankiewicz, Beata and Webb, Penelope M and {Ovarian Cancer Association Consortium}},
doi = {10.1093/ije/dyw158},
file = {:home/riku/Documents/Mendeley Desktop/Dixon et al/Dixon et al.{\_}2016{\_}Adult body mass index and risk of ovarian cancer by subtype a Mendelian randomization study.pdf:pdf},
issn = {1464-3685},
journal = {Int. J. Epidemiol.},
keywords = {Body mass index,Mendelian randomization analysis,obesity,ovarian neoplasms},
pages = {1--12},
pmid = {27401727},
title = {{Adult body mass index and risk of ovarian cancer by subtype: a Mendelian randomization study.}},
year = {2016}
}
@article{Jenabi2011,
abstract = {Conflict and different studies was done about the effect of body mass index on delivery outcomes. Our objective was to effect body mass index on delivery outcomes in hospital of Tamin Ejtemaee in city of Hamedan. Women admitted in unit of labor were invited to participate in this study. During a 3-mounth period, 1272 eligible women gave consent and were randomized in this study. Chi square test and wilcoxon were used for data's analyze. Obesity and overweight of pregnancy was significant correlation with the before parity, increase of weight neonate, gestational age, duration of active phase and second stage of labor. Overweight and obesity pregnancy is associated with adverse pregnancy outcome in women. ?? 2011 Published by Elsevier Ltd.},
author = {Jenabi, Ensiyeh and AslToghiri, Maryam},
doi = {10.1016/j.sbspro.2011.11.089},
file = {:home/riku/Documents/Mendeley Desktop/Jenabi, AslToghiri/Jenabi, AslToghiri{\_}2011{\_}The effect of body mass index on delivery outcomes.pdf:pdf},
issn = {18770428},
journal = {Procedia - Soc. Behav. Sci.},
keywords = {Body Mass Index,Caesarean section,Delivery outcomes,Gestational age,Neonate weight},
pages = {465--469},
publisher = {Elsevier Ltd},
title = {{The effect of body mass index on delivery outcomes}},
volume = {28},
year = {2011}
}
@article{Law2014,
abstract = {New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods.},
author = {Law, Charity W. and Chen, Yunshun and Shi, Wei and Smyth, Gordon K.},
doi = {10.1186/gb-2014-15-2-r29},
file = {:home/riku/Documents/Mendeley Desktop/Law et al/Law et al.{\_}2014{\_}voom precision weights unlock linear model analysis tools for RNA-seq read counts.pdf:pdf},
isbn = {1465-6906},
issn = {1474-760X},
journal = {Genome Biol.},
pages = {R29},
pmid = {24485249},
title = {{voom: precision weights unlock linear model analysis tools for RNA-seq read counts}},
url = {http://dx.doi.org/10.1186/gb-2014-15-2-r29{\%}5Cnhttp://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-2-r29{\%}5Cnhttp://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2014-15-2-r29?site=genomebiology.biomedcentral.com},
volume = {15},
year = {2014}
}
@article{Kearney2010,
abstract = {A picture of food consumption (availability) trends and projections to 2050, both globally and for different regions of the world, along with the drivers largely responsible for these observed consumption trends are the subject of this review. Throughout the world, major shifts in dietary patterns are occurring, even in the consumption of basic staples towards more diversified diets. Accompanying these changes in food consumption at a global and regional level have been considerable health consequences. Populations in those countries undergoing rapid transition are experiencing nutritional transition. The diverse nature of this transition may be the result of differences in socio-demographic factors and other consumer characteristics. Among other factors including urbanization and food industry marketing, the policies of trade liberalization over the past two decades have implications for health by virtue of being a factor in facilitating the 'nutrition transition' that is associated with rising rates of obesity and chronic diseases such as cardiovascular disease and cancer. Future food policies must consider both agricultural and health sectors, thereby enabling the development of coherent and sustainable policies that will ultimately benefit agriculture, human health and the environment.},
author = {Kearney, John},
doi = {10.1098/rstb.2010.0149},
file = {:home/riku/Documents/Mendeley Desktop/Kearney/Kearney{\_}2010{\_}Food consumption trends and drivers.pdf:pdf},
isbn = {1471-2970 (Electronic)$\backslash$r0962-8436 (Linking)},
issn = {0962-8436},
journal = {Philos. Trans. R. Soc. B Biol. Sci.},
keywords = {Agriculture,Food Supply,Humans,Nutrition Policy,Nutritional Status,obesity},
mendeley-tags = {obesity},
number = {1554},
pages = {2793--2807},
pmid = {20713385},
title = {{Food consumption trends and drivers}},
volume = {365},
year = {2010}
}
@misc{Carlson2016,
author = {Carlson, M},
title = {{GO.db: A set of annotation maps describing the entire Gene Ontology. R package version 3.4.0}},
year = {2016}
}
@article{Giovannucci1995,
author = {Giovannucci, Edward},
file = {:home/riku/Documents/Mendeley Desktop/Giovannucci/Giovannucci{\_}1995{\_}Insulin and colon cancer.pdf:pdf},
journal = {Cancer Causes Control},
keywords = {colon cancer,diet,hyperinsulinemia,insulin,insulin cancer hypothesis,obesity,physical inactivity},
mendeley-tags = {insulin cancer hypothesis},
number = {18},
pages = {164--179},
title = {{Insulin and colon cancer}},
volume = {6},
year = {1995}
}
@article{Pulgaron2014,
author = {Pulgar{\'{o}}n, Elizabeth R.},
doi = {10.1016/j.clinthera.2012.12.014.Childhood},
file = {:home/riku/Documents/Mendeley Desktop/Pulgar{\'{o}}n/Pulgar{\'{o}}n{\_}2014{\_}Childhood Obesity A Review of Increased Risk for Physical and Psychological Co-morbidities.pdf:pdf},
isbn = {3052430807},
journal = {Clin. Ther.},
keywords = {2013 excerpta medica,all correspondence concerning this,all rights reserved,article should be addressed,childhood obesity,department of pediatrics,division of,inc,medical co-morbidities,obesity,phd,psychological co-morbidities,pulgaron,to elizabeth r},
mendeley-tags = {obesity},
pages = {1--21},
title = {{Childhood Obesity: A Review of Increased Risk for Physical and Psychological Co-morbidities}},
volume = {35},
year = {2014}
}
@article{Spiegelman2001,
abstract = {Obesity is defined medically as a state of increased body weight, more specifically adipose tissue, of sufficient magnitude to produce adverse health consequences. There has been an alarming increase recently in the prevalence of this heterogeneous group of disorders in the Western world (Kuczmarski et al., 1994). Fully one- third of the American population is now considered obese, and the prevalence of obesity in children is esca- lating dramatically, presaging even greater medical harm in the decades to come (Troiano and Flegal, 1999). What accounts for this epidemic of energy storage? Bodyweight and composition, andthe storage of energy as triglyceride in adipose tissue, are determined by the interaction between genetic, environmental, and psy- chosocial factors. These influences ultimately act by changing the energy balance equation, that is, the long- term balance between energy intake and expenditure. Physiologic studies had previously suggested that body weight and energy stores are homeostatically regulated, with either weight loss or gain producing concerted changes in energy intake and expenditure that resist the initial perturbation. Recent cloning of several obesity genes has revealed the initial molecular components of a coherent physiologic system for energy homeostasis (Barsh et al., 2000). Studies of obesity pathogenesis must now attempt to explain the disorder in the context of this physiologic system.},
author = {Spiegelman, Bruce M. and Flier, Jeffrey S.},
doi = {10.1016/S0092-8674(01)00240-9},
file = {:home/riku/Documents/Mendeley Desktop/Spiegelman, Flier/Spiegelman, Flier{\_}2001{\_}Obesity and the regulation of energy balance.pdf:pdf},
isbn = {0092-8674},
issn = {00928674},
journal = {Cell},
keywords = {obesity},
mendeley-tags = {obesity},
number = {4},
pages = {531--543},
pmid = {11239410},
title = {{Obesity and the regulation of energy balance}},
volume = {104},
year = {2001}
}
@article{Perez-Solis2016,
author = {P{\'{e}}rez-Solis, Marco All{\'{a}}n and Maya-Nu{\~{n}}ez, Guadalupe and Casas-Gonz{\'{a}}lez, Patricia and Olivares, Aleida and Aguilar-Rojas, Arturo},
doi = {10.1186/s12935-016-0284-7},
file = {:home/riku/Documents/Mendeley Desktop/P{\'{e}}rez-Solis et al/P{\'{e}}rez-Solis et al.{\_}2016{\_}Effects of the lifestyle habits in breast cancer transcriptional regulation.pdf:pdf},
issn = {1475-2867},
journal = {Cancer Cell Int.},
keywords = {Breast cancer,Ethanol,Obesity,Tobacco,Transcription,breast cancer,ethanol,obesity,tobacco,transcription},
pages = {7},
publisher = {BioMed Central},
title = {{Effects of the lifestyle habits in breast cancer transcriptional regulation}},
volume = {16},
year = {2016}
}
@article{Arem2013,
abstract = {Background Higher body mass index (BMI) and inactivity have been associated with a higher risk of developing endometrial cancer, but the impact on endometrial cancer survival is unclear. Methods Among incident endometrial cancer case subjects in the National Institutes of Health-AARP Diet and Health Study, we examined associations of prediagnosis BMI (n = 1400) and physical activity (n = 875) with overall and disease-specific 5- and 10-year mortality. Using Cox proportional hazards regression, we estimated hazard ratios (HRs) and 95{\%} confidence intervals (CIs), adjusting for tumor characteristics, treatment, and other risk factors. All statistical tests were two-sided. Results Compared with women with a BMI in the range of 18.5 to less than 25kg/m(2), the hazard ratios for 5-year all-cause mortality were 1.74 (95{\%} CI = 1.13 to 2.66) for BMI in the range of 25 to less than 30kg/m(2), 1.84 (95{\%} CI = 1.17 to 2.88) for BMI in the range of 30 to less than 35kg/m(2), and 2.35 (95{\%} CI = 1.48 to 3.73) for BMI greater than or equal to 35kg/m(2) (P trend {\textless} .001). Higher BMI was also statistically significantly associated with poorer endometrial cancer-specific but not cardiovascular disease 5-year mortality. Hazard ratio estimates for 10-year all-cause and endometrial cancer-specific mortality as related to BMI were similar to 5-year hazard ratio estimates, whereas 10-year cardiovascular disease mortality became statistically significant (HR = 4.08; 95{\%} CI = 1.56 to 10.71 comparing extreme BMI groups). More physical activity was related to lower all-cause 5-year mortality (HR = 0.57, 95{\%} CI = 0.33 to 0.98 for {\textgreater}7 hours/week vs never/rarely), but the association was attenuated after adjustment for BMI (HR = 0.64, 95{\%} CI = 0.37 to 1.12). No association was observed between physical activity and disease-specific mortality. Conclusions Our findings suggest that higher prediagnosis BMI increases risk of overall and disease-specific mortality among women diagnosed with endometrial cancer, whereas physical activity lowers risk. Intervention studies of the effect of these modifiable lifestyle factors on mortality are needed.},
author = {Arem, Hannah and Park, Yikyung and Pelser, Colleen and Ballard-Barbash, Rachel and Irwin, Melinda L. and Hollenbeck, Albert and Gierach, Gretchen L. and Brinton, Louise a. and Pfeiffer, Ruth M. and Matthews, Charles E.},
doi = {10.1093/jnci/djs530},
file = {:home/riku/Documents/Mendeley Desktop/Arem et al/Arem et al.{\_}2013{\_}Prediagnosis body mass index, physical activity, and mortality in endometrial cancer patients.pdf:pdf},
isbn = {1460-2105 (Electronic)$\backslash$r0027-8874 (Linking)},
issn = {00278874},
journal = {J. Natl. Cancer Inst.},
number = {5},
pages = {342--349},
pmid = {23297041},
title = {{Prediagnosis body mass index, physical activity, and mortality in endometrial cancer patients}},
volume = {105},
year = {2013}
}
@article{Ritchie2015,
author = {Ritchie, Matthew E and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W and Shi, Wei and Smyth, Gordon K},
doi = {10.1093/nar/gkv007},
file = {:home/riku/Documents/Mendeley Desktop/Ritchie et al/Ritchie et al.{\_}2015{\_}limma powers differential expression analyses for RNA-sequencing and microarray studies.pdf:pdf},
number = {7},
pages = {1--13},
title = {{limma powers differential expression analyses for RNA-sequencing and microarray studies}},
volume = {43},
year = {2015}
}
@article{Shaffer1995,
author = {Shaffer, Juliet Popper},
doi = {10.1016/S1573-4412(84)02006-7},
file = {:home/riku/Documents/Mendeley Desktop/Shaffer/Shaffer{\_}1995{\_}Multiple hypothesis testing.pdf:pdf},
isbn = {9780444861863},
issn = {15734412},
journal = {Annu. Rev. Psychol.},
pages = {561--584},
title = {{Multiple hypothesis testing}},
volume = {46},
year = {1995}
}
@book{Hochberg1987,
address = {New York},
author = {Hochberg, Yosef and Tamhane, Ajit C.},
publisher = {John Wiley and Sons},
title = {{Multiple comparison procedures}},
year = {1987}
}
@article{Metzker2010,
abstract = {Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.},
archivePrefix = {arXiv},
arxivId = {209},
author = {Metzker, Michael L},
doi = {10.1038/nrg2626},
eprint = {209},
file = {:home/riku/Documents/Mendeley Desktop/Metzker/Metzker{\_}2010{\_}Sequencing technologies - the next generation.pdf:pdf},
isbn = {1471-0056},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
number = {1},
pages = {31--46},
pmid = {19997069},
publisher = {Nature Publishing Group},
title = {{Sequencing technologies - the next generation.}},
volume = {11},
year = {2010}
}
@article{Bild2009,
abstract = {INTRODUCTION: Perhaps the major challenge in developing more effective therapeutic strategies for the treatment of breast cancer patients is confronting the heterogeneity of the disease, recognizing that breast cancer is not one disease but multiple disorders with distinct underlying mechanisms. Gene-expression profiling studies have been used to dissect this complexity, and our previous studies identified a series of intrinsic subtypes of breast cancer that define distinct populations of patients with respect to survival. Additional work has also used signatures of oncogenic pathway deregulation to dissect breast cancer heterogeneity as well as to suggest therapeutic opportunities linked to pathway activation. METHODS: We used genomic analyses to identify relations between breast cancer subtypes, pathway deregulation, and drug sensitivity. For these studies, we use three independent breast cancer gene-expression data sets to measure an individual tumor phenotype. Correlation between pathway status and subtype are examined and linked to predictions for response to conventional chemotherapies. RESULTS: We reveal patterns of pathway activation characteristic of each molecular breast cancer subtype, including within the more aggressive subtypes in which novel therapeutic opportunities are critically needed. Whereas some oncogenic pathways have high correlations to breast cancer subtype (RAS, CTNNB1, p53, HER1), others have high variability of activity within a specific subtype (MYC, E2F3, SRC), reflecting biology independent of common clinical factors. Additionally, we combined these analyses with predictions of sensitivity to commonly used cytotoxic chemotherapies to provide additional opportunities for therapeutics specific to the intrinsic subtype that might be better aligned with the characteristics of the individual patient. CONCLUSIONS: Genomic analyses can be used to dissect the heterogeneity of breast cancer. We use an integrated analysis of breast cancer that combines independent methods of genomic analyses to highlight the complexity of signaling pathways underlying different breast cancer phenotypes and to identify optimal therapeutic opportunities.},
author = {Bild, A H and Parker, J S and Gustafson, A M and Acharya, C R and Hoadley, K A and Anders, C and Marcom, P K and Carey, L A and Potti, A and Nevins, J R and Perou, C M},
doi = {10.1186/bcr2344},
file = {:home/riku/Documents/Mendeley Desktop/Bild et al/Bild et al.{\_}2009{\_}An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for b.pdf:pdf},
isbn = {1465-542X (Electronic)$\backslash$r1465-5411 (Linking)},
issn = {1465-542X},
journal = {Breast cancer Res.},
keywords = {*Genetic Heterogeneity,*Oligonucleotide Array Sequence Analysis,Antineoplastic Agents/pharmacology/therapeutic use,Biological/biosynthesis/*genetics,Breast Neoplasms/classification/drug therapy/*gene,Cytotoxins/pharmacology/therapeutic use,Databases,Drug Resistance,Factual,Female,Gene Expression Profiling/*methods,Gene Expression Regulation,Gene Regulatory Networks/genetics,Humans,Metabolic Networks and Pathways/genetics,Neoplasm Proteins/biosynthesis/*genetics,Neoplasm/genetics,Neoplastic,Oncogenes,Phenotype,Signal Transduction/genetics,Tumor Markers},
number = {4},
pages = {R55},
pmid = {19638211},
title = {{An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer}},
volume = {11},
year = {2009}
}
@article{Joshi2005,
abstract = {Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes. Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways. The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle. Reactome provides a qualitative framework, on which quantitative data can be superimposed. Tools have been developed to facilitate custom data entry and annotation by expert biologists, and to allow visualization and exploration of the finished dataset as an interactive process map. Although our primary curational domain is pathways from Homo sapiens, we regularly create electronic projections of human pathways onto other organisms via putative orthologs, thus making Reactome relevant to model organism research communities. The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed.},
author = {Joshi-Tope, G. and Gillespie, M. and Vastrik, I. and D{\&}apos;Eustachio, P. and Schmidt, E. and de Bono, B. and Jassal, B. and Gopinath, G. R. and Wu, G. R. and Matthews, L. and Lewis, S. and Birney, E. and Stein, L.},
doi = {10.1093/nar/gki072},
file = {:home/riku/Documents/Mendeley Desktop/Joshi-Tope et al/Joshi-Tope et al.{\_}2005{\_}Reactome A knowledgebase of biological pathways.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {DATABASE ISS.},
pages = {D428--D432},
pmid = {15608231},
title = {{Reactome: A knowledgebase of biological pathways}},
volume = {33},
year = {2005}
}
@article{Edgar2002,
abstract = {The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.},
author = {Edgar, Ron and Domrachev, Michael and Lash, Alex E},
doi = {10.1093/nar/30.1.207},
file = {:home/riku/Documents/Mendeley Desktop/Edgar, Domrachev, Lash/Edgar, Domrachev, Lash{\_}2002{\_}Gene Expression Omnibus NCBI gene expression and hybridization array data repository.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
number = {1},
pages = {207--210},
pmid = {11752295},
title = {{Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.}},
volume = {30},
year = {2002}
}
@article{Khatri2005,
abstract = {Independent of the platform and the analysis methods used, the result of a microarray experiment is, in most cases, a list of differentially expressed genes. An automatic ontological analysis approach has been recently proposed to help with the biological interpretation of such results. Currently, this approach is the de facto standard for the secondary analysis of high throughput experiments and a large number of tools have been developed for this purpose. We present a detailed comparison of 14 such tools using the following criteria: scope of the analysis, visualization capabilities, statistical model(s) used, correction for multiple comparisons, reference microarrays available, installation issues and sources of annotation data. This detailed analysis of the capabilities of these tools will help researchers choose the most appropriate tool for a given type of analysis. More importantly, in spite of the fact that this type of analysis has been generally adopted, this approach has several important intrinsic drawbacks. These drawbacks are associated with all tools discussed and represent conceptual limitations of the current state-of-the-art in ontological analysis. We propose these as challenges for the next generation of secondary data analysis tools.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Khatri, Purvesh and Drǎghici, Sorin},
doi = {10.1093/bioinformatics/bti565},
eprint = {NIHMS150003},
file = {:home/riku/Documents/Mendeley Desktop/Khatri, Drǎghici/Khatri, Drǎghici{\_}2005{\_}Ontological analysis of gene expression data Current tools, limitations, and open problems.pdf:pdf},
isbn = {1367-4803 (Print)$\backslash$r1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {18},
pages = {3587--3595},
pmid = {15994189},
title = {{Ontological analysis of gene expression data: Current tools, limitations, and open problems}},
volume = {21},
year = {2005}
}
@article{Franks2010,
author = {Franks, Paul W. and Hanson, Robert L. and Knowler, William C. and Sievers, Maurice L. and Bennett, Peter H. and Looker, Helen C.},
doi = {10.1056/NEJMoa0810625)},
file = {:home/riku/Documents/Mendeley Desktop/Franks et al/Franks et al.{\_}2010{\_}Childhood obesity, other cardiovascular risk factors, and premature death.pdf:pdf},
journal = {N. Engl. J. Med.},
keywords = {obesity},
mendeley-tags = {obesity},
number = {6},
pages = {485--493},
title = {{Childhood obesity, other cardiovascular risk factors, and premature death}},
volume = {362},
year = {2010}
}
@article{WHO2000,
author = {{World Health Organisation}},
doi = {10.1016/S0140-6736(03)15268-3},
file = {:home/riku/Documents/Mendeley Desktop/World Health Organisation/World Health Organisation{\_}2000{\_}Obesity preventing and managing the global epidemic.pdf:pdf;:home/riku/Documents/Mendeley Desktop/World Health Organisation/World Health Organisation{\_}2000{\_}Obesity preventing and managing the global epidemic(2).pdf:pdf;:home/riku/Documents/Mendeley Desktop/World Health Organisation/World Health Organisation{\_}2000{\_}Obesity preventing and managing the global epidemic(3).pdf:pdf},
isbn = {9241208945},
issn = {0512-3054},
keywords = {obesity},
mendeley-tags = {obesity},
pages = {6--8},
pmid = {11234459},
title = {{Obesity : preventing and managing the global epidemic}},
volume = {894},
year = {2000}
}
@article{GO2004,
abstract = {The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.},
author = {{Gene Ontology Consortium}},
doi = {10.1093/nar/gkh036},
file = {:home/riku/Documents/Mendeley Desktop/Gene Ontology Consortium/Gene Ontology Consortium{\_}2004{\_}The Gene Ontology (GO) database and informatics resource.pdf:pdf},
isbn = {1362-4962 (Electronic)},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
number = {Database issue},
pages = {258D--261},
pmid = {14681407},
title = {{The Gene Ontology (GO) database and informatics resource.}},
volume = {32},
year = {2004}
}
@article{Yusuf2005,
abstract = {BACKGROUND: Obesity is a major risk factor for cardiovascular disease, but the most predictive measure for different ethnic populations is not clear. We aimed to assess whether markers of obesity, especially waist-to-hip ratio, would be stronger indicators of myocardial infarction than body-mass index (BMI), the conventional measure. METHODS: We did a standardised case-control study of acute myocardial infarction with 27 098 participants in 52 countries (12,461 cases and 14,637 controls) representing several major ethnic groups. We assessed the relation between BMI, waist and hip circumferences, and waist-to-hip ratio to myocardial infarction overall and for each group. FINDINGS: BMI showed a modest and graded association with myocardial infarction (OR 1.44, 95{\%} CI 1.32-1.57 top quintile vs bottom quintile before adjustment), which was substantially reduced after adjustment for waist-to-hip ratio (1.12, 1.03-1.22), and non-significant after adjustment for other risk factors (0.98, 0.88-1.09). For waist-to-hip ratio, the odds ratios for every successive quintile were significantly greater than that of the previous one (2nd quintile: 1.15, 1.05-1.26; 3rd quintile: 1.39; 1.28-1.52; 4th quintile: 1.90, 1.74-2.07; and 5th quintiles: 2.52, 2.31-2.74 [adjusted for age, sex, region, and smoking]). Waist (adjusted OR 1.77; 1.59-1.97) and hip (0.73; 0.66-0.80) circumferences were both highly significant after adjustment for BMI (p{\textless}0.0001 top vs bottom quintiles). Waist-to-hip ratio and waist and hip circumferences were closely (p{\textless}0.0001) associated with risk of myocardial infarction even after adjustment for other risk factors (ORs for top quintile vs lowest quintiles were 1.75, 1.33, and 0.76, respectively). The population-attributable risks of myocardial infarction for increased waist-to-hip ratio in the top two quintiles was 24.3{\%} (95{\%} CI 22.5-26.2) compared with only 7.7{\%} (6.0-10.0) for the top two quintiles of BMI. INTERPRETATION: Waist-to-hip ratio shows a graded and highly significant association with myocardial infarction risk worldwide. Redefinition of obesity based on waist-to-hip ratio instead of BMI increases the estimate of myocardial infarction attributable to obesity in most ethnic groups.},
author = {Yusuf, Salim and Hawken, Steven and Ounpuu, Stephanie and Bautista, Leonelo and Franzosi, Maria Grazia and Commerford, Patrick and Lang, Chim C and Rumboldt, Zvonko and Onen, Churchill L and Lisheng, Liu and Tanomsup, Supachai and Wangai, Paul and Razak, Fahad and Sharma, Arya M and Anand, Sonia S},
doi = {10.1016/S0140-6736(05)67663-5},
file = {:home/riku/Documents/Mendeley Desktop/Yusuf et al/Yusuf et al.{\_}2005{\_}Obesity and the risk of myocardial infarction in 27,000 participants from 52 countries a case-control study.pdf:pdf},
isbn = {1474-547X},
issn = {1474-547X},
journal = {Lancet},
keywords = {obesity},
mendeley-tags = {obesity},
number = {9497},
pages = {1640--1649},
pmid = {16271645},
title = {{Obesity and the risk of myocardial infarction in 27,000 participants from 52 countries: a case-control study.}},
volume = {366},
year = {2005}
}
@misc{hgu133,
author = {Carlson, M},
title = {{hgu133a.db: Affymetrix Human Genome U133 Set annotation data (chip hgu133a). R package version 3.2.3}},
year = {2016}
}
@article{WHO2010,
abstract = {In May 2004, the 57th World Health Assembly (WHA) endorsed the World Health Organization (WHO) Global Strategy on Diet, Physical Activity and Health. The Strategy was developed through a wide-ranging series of consultations with all concerned stakeholders in response to a request from Member States at World Health Assembly 2002 (Resolution WHA55.23). The Strategy, together with the Resolution by which it was endorsed (WHA57.17), are contained in this document.},
archivePrefix = {arXiv},
arxivId = {arXiv:gr-qc/9809069v1},
author = {{World Health Organisation}},
doi = {10.1080/11026480410034349},
eprint = {9809069v1},
file = {:home/riku/Documents/Mendeley Desktop/World Health Organisation/World Health Organisation{\_}2010{\_}Global recommendations on physical activity for health.pdf:pdf},
isbn = {978 92 4 159 997 9},
issn = {11026480},
journal = {Geneva World Heal. Organ.},
keywords = {obesity},
mendeley-tags = {obesity},
pages = {60},
pmid = {20963782},
primaryClass = {arXiv:gr-qc},
title = {{Global recommendations on physical activity for health}},
year = {2010}
}
@article{McLaren2007,
abstract = {The objective of this review was to update Sobal and Stunkard's exhaustive review of the literature on the relation between socioeconomic status (SES) and obesity (Psychol Bull 1989;105:260–75). Diverse research databases (including CINAHL, ERIC, MEDLINE, and Social Science Abstracts) were comprehensively searched during the years 1988–2004 inclusive, using “obesity,” “socioeconomic status,” and synonyms as search terms. A total of 333 published studies, representing 1,914 primarily cross-sectional associations, were included in the review. The overall pattern of results, for both men and women, was of an increasing proportion of positive associations and a decreasing proportion of negative associations as one moved from countries with high levels of socioeconomic development to countries with medium and low levels of development. Findings varied by SES indicator; for example, negative associations (lower SES associated with larger body size) for women in highly developed countries were most common with education and occupation, while positive associations for women in medium- and low-development countries were most common with income and material possessions. Patterns for women in higher- versus lower-development countries were generally less striking than those observed by Sobal and Stunkard; this finding is interpreted in light of trends related to globalization. Results underscore a view of obesity as a social phenomenon, for which appropriate action includes targeting both economic and sociocultural factors.},
author = {McLaren, Lindsay},
doi = {10.1093/epirev/mxm001},
file = {:home/riku/Documents/Mendeley Desktop/McLaren/McLaren{\_}2007{\_}Socioeconomic status and obesity.pdf:pdf},
isbn = {9780199940684},
issn = {0193936X},
journal = {Epidemiol. Rev.},
keywords = {Developing countries,Obesity,Review [publication type],Sex,Social class,obesity},
mendeley-tags = {obesity},
pages = {29--48},
pmid = {17478442},
title = {{Socioeconomic status and obesity}},
volume = {29},
year = {2007}
}
@article{Frayling2007,
abstract = {Obesity is a serious international health problem that increases the risk of several common diseases. The genetic factors predisposing to obesity are poorly understood. A genome-wide search for type 2 diabetes–susceptibility genes identified a common variant in the FTO (fat mass and obesity associated) gene that predisposes to diabetes through an effect on body mass index (BMI). An additive association of the variant with BMI was replicated in 13 cohorts with 38,759 participants. The 16{\%} of adults who are homozygous for the risk allele weighed about 3 kilograms more and had 1.67-fold increased odds of obesity when compared with those not inheriting a risk allele. This association was observed from age 7 years upward and reflects a specific increase in fat mass.},
author = {Frayling, Timothy M. and Timpson, Nicholas J and Weedon, Michael N and Freathy, Rachel M and Lindgren, Cecilia M and Perry, John R B and Katherine, S and Lango, Hana and Rayner, Nigel W and Shields, Beverley and Harries, Lorna W and Barrett, C and Ellard, Sian and Groves, Christopher J and Knight, Bridget and Patch, Ann-marie and Ness, Andrew R and Ebrahim, Shah and Lawlor, Debbie a and Ring, Susan M and Ben-shlomo, Yoav and Jarvelin, Marjo-riitta and Sovio, Ulla and Bennett, Amanda J and Melzer, David and Loos, Ruth J F and Barroso, In{\^{e}}s and Wareham, Nicholas J and Karpe, Fredrik and Owen, Katharine R and Cardon, Lon R and Walker, Mark and Hitman, Graham a and Colin, N a and Doney, Alex S F and Morris, Andrew D and Smith, George Davey and Wellcome, The and Case, Trust and Consortium, Control and Hattersley, Andrew T and Mccarthy, Mark I},
doi = {10.1126/science.1141634},
file = {:home/riku/Documents/Mendeley Desktop/Frayling et al/Frayling et al.{\_}2007{\_}A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity.pdf:pdf},
isbn = {1095-9203 (Electronic)},
issn = {0036-8075},
journal = {Science (80-. ).},
keywords = {FTO,GWAS,obesity},
mendeley-tags = {FTO,GWAS,obesity},
pages = {889--894},
pmid = {17434869},
title = {{A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity}},
volume = {316},
year = {2007}
}
@article{Osborne2011,
abstract = {The estrogen receptor (ER) pathway plays a pivotal role in breast cancer development and progression. Endocrine therapy to block the ER pathway is highly effective, but its usefulness is limited by common intrinsic and acquired resistance. Multiple mechanisms responsible for endocrine resistance have been proposed and include deregulation of various components of the ER pathway itself, alterations in cell cycle and cell survival signaling molecules, and the activation of escape pathways that can provide tumors with alternative proliferative and survival stimuli. Among these, increased expression or signaling of growth factor receptor pathways, especially the EGFR/HER2 pathway, has been associated with both experimental and clinical endocrine therapy resistance. New treatment combinations targeting both ER and growth factor receptor signaling to block the crosstalk between these pathways and eliminate escape routes have been proven highly effective in preclinical models. Results of recent clinical studies, while partly supporting this approach, also highlight the need to better identify a priori the patients whose tumors are most likely to benefit from these specific cotargeting strategies.},
author = {Osborne, C Kent and Schiff, Rachel},
doi = {10.1146/annurev-med-070909-182917},
file = {:home/riku/Documents/Mendeley Desktop/Osborne, Schiff/Osborne, Schiff{\_}2011{\_}Mechanisms of endocrine resistance in breast cancer.pdf:pdf},
isbn = {1545-326X (Electronic)$\backslash$r0066-4219 (Linking)},
issn = {0066-4219},
journal = {Annu. Rev. Med.},
keywords = {combination therapy,crosstalk,endocrine therapy,estrogen receptor,growth factor receptor,signaling},
pages = {233--247},
pmid = {20887199},
title = {{Mechanisms of endocrine resistance in breast cancer.}},
volume = {62},
year = {2011}
}
@article{Hanahan2000,
author = {Hanahan, Douglas and Weinberg, Robert A.},
doi = {10.1016/S0092-8674(00)81683-9},
file = {:home/riku/Documents/Mendeley Desktop/Hanahan, Weinberg/Hanahan, Weinberg{\_}2000{\_}The hallmarks of cancer.pdf:pdf},
isbn = {0026201009680},
issn = {00928674},
journal = {Cell},
keywords = {Key Paper},
mendeley-tags = {Key Paper},
pages = {57--70},
pmid = {19636327},
title = {{The hallmarks of cancer}},
volume = {100},
year = {2000}
}
@article{Neel1962,
abstract = {FOR THE POPULATION GENETICIST, diabetes mellitus has long presented an enigma. Here is a relatively frequent disease, often interfering with reproduction by virtue of an onset during the reproductive or even pre-reproductive years, with a well-defined genetic basis, perhaps as simple in many families as a single recessive or incompletely recessive gene (cf. Allan, 1933; Pincus and White, 1933, 1934; Harris, 1950; Steinberg and Wilder, 1952; Lamy, Frezal and de Grouchy, 1957; Steinberg, 1959; Post, 1962a). If the considerable frequency of the disease is of relatively long duration in the history of our species, how can this be accounted for in the face of the obvious and strong genetic selection against the condition? If, on the other hand, this frequency is a relatively recent phenomenon, what changes in the environment are responsible for the increase? Current developments in the study of this disease suggest an explanation with important biological ramifications.},
author = {Neel, J. V.},
doi = {10.1007/SpringerReference_98337},
file = {:home/riku/Documents/Mendeley Desktop/Neel/Neel{\_}1962{\_}Diabetes mellitus a thrifty genotype rendered detrimental by progress 1962.pdf:pdf},
isbn = {0002929700029297},
issn = {00429686},
journal = {Am. J. Hum. Genet.},
keywords = {obesity},
mendeley-tags = {obesity},
number = {4},
pages = {353--362},
pmid = {13937884},
title = {{Diabetes mellitus: a "thrifty" genotype rendered detrimental by "progress"? 1962.}},
volume = {14},
year = {1962}
}
@article{Kublaoui2006,
abstract = {Single-minded 1 (SIM1) mutations are associated with obesity in mice and humans. Haploinsufficiency of mouse Sim1 causes hyperphagic obesity with increased linear growth and enhanced sensitivity to a high-fat diet, a phenotype similar to that of agouti yellow and melanocortin 4 receptor knockout mice. To investigate the effects of increased Sim1 dosage, we generated transgenic mice that overexpress human SIM1 and examined their phenotype. Compared with wild-type mice, SIM1 transgenic mice had no obvious phenotype on a low-fat chow diet but were resistant to diet-induced obesity on a high-fat diet due to reduced food intake with no change in energy expenditure. The SIM1 transgene also completely rescued the hyperphagia and partially rescued the obesity of agouti yellow mice, in which melanocortin signaling is abrogated. Our results indicate that the melanocortin 4 receptor signals through Sim1 or its transcriptional targets in controlling food intake but not energy expenditure.},
author = {Kublaoui, Bassil M. and Holder, J. Lloyd and Tolson, Kristen P. and Gemelli, Terry and Zinn, Andrew R.},
doi = {10.1210/en.2006-0453},
file = {:home/riku/Documents/Mendeley Desktop/Kublaoui et al/Kublaoui et al.{\_}2006{\_}SIM1 overexpression partially rescues agouti yellow and diet-induced obesity by normalizing food intake.pdf:pdf},
isbn = {0013-7227 (Print)$\backslash$r0013-7227 (Linking)},
issn = {00137227},
journal = {Endocrinology},
keywords = {obesity},
mendeley-tags = {obesity},
number = {10},
pages = {4542--4549},
pmid = {16709610},
title = {{SIM1 overexpression partially rescues agouti yellow and diet-induced obesity by normalizing food intake}},
volume = {147},
year = {2006}
}
@article{Challis2002,
abstract = {The functional loss of both alleles of the human pro-opiomelanocortin (POMC) gene leads to a very rare syndrome of hypoadrenalism, red hair and early-onset obesity. In order to examine whether more subtle genetic variants in POMC might contribute to early-onset obesity, the coding region of the gene was sequenced in 262 Caucasian subjects with a history of severe obesity from childhood. Two children were found to be heterozygous for a missense mutation, R236G, which disrupts the dibasic cleavage site between beta melanocyte-stimulating hormone (beta-MSH) and beta-endorphin. Beta-TC3 cells transfected with the mutant POMC cDNA produced a mutant beta-MSH/beta-endorphin fusion protein. This fusion protein bound to the human melanocortin-4 receptor (hMC4R) with an affinity similar to its natural ligands, but had a markedly reduced ability to activate the receptor. This variant co-segregated with early-onset obesity over three generations in one family and was absent in 412 normal weight UK Caucasian controls. Combining the results in UK Caucasians with a new case-control study in French subjects and three previously published reports, mutations disrupting this processing site were present in 0.88{\%} of subjects with early-onset obesity and 0.22{\%} of normal-weight controls. These results suggest that the R236G mutation may confer an inherited susceptibility to obesity through the production of an aberrant fusion protein that has the capacity to interfere with central melanocortin signalling.},
author = {Challis, Benjamin G and Pritchard, Lynn E and Creemers, John W M and Delplanque, Jerome and Keogh, Julia M and Luan, Jian'an and Wareham, Nicholas J and Yeo, Giles S H and Bhattacharyya, Sumit and Froguel, Phillipe and White, Anne and Farooqi, I Sadaf and O'Rahilly, Stephen},
doi = {10.1186/1746-6148-8-111},
file = {:home/riku/Documents/Mendeley Desktop/Challis et al/Challis et al.{\_}2002{\_}A missense mutation disrupting a dibasic prohormone processing site in pro-opiomelanocortin (POMC) increases suscept.pdf:pdf},
isbn = {0964-6906 (Print)$\backslash$n0964-6906 (Linking)},
issn = {0964-6906},
journal = {Hum. Mol. Genet.},
keywords = {Adolescent,Adrenal Insufficiency,Adrenal Insufficiency: genetics,Animals,CHO Cells,Case-Control Studies,Corticotropin,Corticotropin: metabolism,Cricetinae,DNA Mutational Analysis,DNA Primers,DNA Primers: chemistry,Disease Susceptibility,Female,Hair Color,Hair Color: genetics,Humans,Male,Melanocortin,Missense,Missense: genetics,Mutation,Obesity,Obesity: etiology,Obesity: genetics,Pedigree,Peptide Fragments,Peptide Fragments: chemical synthesis,Peptide Fragments: metabolism,Polymerase Chain Reaction,Polymorphism,Precipitin Tests,Pro-Opiomelanocortin,Pro-Opiomelanocortin: genetics,Receptor,Receptors,Recombinant Fusion Proteins,Recombinant Fusion Proteins: metabolism,Restriction Fragment Length,Type 4,beta-Endorphin,beta-Endorphin: metabolism,beta-MSH,beta-MSH: metabolism,obesity},
mendeley-tags = {obesity},
number = {17},
pages = {1997--2004},
pmid = {12165561},
title = {{A missense mutation disrupting a dibasic prohormone processing site in pro-opiomelanocortin (POMC) increases susceptibility to early-onset obesity through a novel molecular mechanism.}},
volume = {11},
year = {2002}
}
@book{Garrow1988,
address = {London},
author = {Garrow, J. S.},
keywords = {obesity},
mendeley-tags = {obesity},
pages = {1--16},
publisher = {Churchill Livingstone},
title = {{Obesity and related diseases}},
year = {1988}
}
@article{Dubern2001,
abstract = {OBJECTIVE: To search for mutations in melanocortin pathway elements, that is, the melanocortin-4 receptor (MC4R), agouti-related protein (AGRP), and alpha-melanocyte-stimulating hormone (alpha MSH) genes in children with severe obesity. STUDY DESIGN: Direct sequencing of the MC4R encoding sequence and single-strand polymorphism conformation analysis of AGRP and alpha MSH genes were performed in 63 severely obese children. Polymerase chain reaction (PCR) assays of restriction fragment length polymorphism were used to assess the frequency of each newly discovered mutation in 283 non-obese control subjects. RESULTS: Four dominantly inherited, heterozygous, missense MC4R mutations (Val50Met, Ser58Cys, Ile102Ser, and Ile170Val) were identified in 4 unrelated children and none of the control subjects. Expression of the obese phenotype was variable in mutation-positive family members. Clinical and laboratory features were similar in the obese children with and without an MC4R mutation. Two polymorphisms were detected in the AGRP -encoding sequence (a silent mutation in exon 1 and Ala67Thr in exon 2), with similar frequencies in the obese and control groups. No mutations were found in the alpha MSH gene. CONCLUSIONS: MC4R mutations may be a non-negligible cause of severe obesity in children with variable expression and penetrance. Mutations in AGRP and alpha MSH genes were not among the causes of obesity in our population.},
author = {Dubern, B and Cl{\'{e}}ment, K and Pelloux, V and Froguel, P and Girardet, J P and Guy-Grand, B and Tounian, P},
doi = {10.1067/mpd.2001.116284},
file = {:home/riku/Documents/Mendeley Desktop/Dubern et al/Dubern et al.{\_}2001{\_}Mutational analysis of melanocortin-4 receptor, agouti-related protein, and alpha-melanocyte-stimulating hormone gene.pdf:pdf},
isbn = {0022-3476},
issn = {0022-3476},
journal = {J. Pediatr.},
keywords = {obesity},
mendeley-tags = {obesity},
number = {2},
pages = {204--209},
pmid = {11487744},
title = {{Mutational analysis of melanocortin-4 receptor, agouti-related protein, and alpha-melanocyte-stimulating hormone genes in severely obese children.}},
volume = {139},
year = {2001}
}
@article{Freedman2001,
abstract = {BACKGROUND: Childhood obesity is related to adult levels of lipids, lipoproteins, blood pressure, and insulin and to morbidity from coronary heart disease (CHD). However, the importance of the age at which obesity develops in these associations remains uncertain. OBJECTIVE AND DESIGN: We assessed the longitudinal relationship of childhood body mass index (BMI, kg/m(2)) to adult levels of lipids, insulin, and blood pressure among 2617 participants. All participants were initially examined at ages 2 to 17 years and were reexamined at ages 18 to 37 years; the mean follow-up was 17 years. RESULTS: Of the overweight children (BMI {\textgreater}/=95th percentile), 77{\%} remained obese ({\textgreater}/=30 kg/m(2)) as adults. Childhood overweight was related to adverse risk factor levels among adults, but associations were weak (r {\~{}} 0.1-0.3) and were attributable to the strong persistence of weight status between childhood and adulthood. Although obese adults had adverse levels of lipids, insulin, and blood pressure, levels of these risk factors did not vary with childhood weight status or with the age ({\textless}/=8 years, 12-17 years, or {\textgreater}/=18 years) of obesity onset. CONCLUSIONS: Additional data are needed to assess the independent relationship of childhood weight status to CHD morbidity. Because normal-weight children who become obese adults have adverse risk factor levels and probably will be at increased risk for adult morbidity, our results emphasize the need for both primary and secondary prevention.},
author = {Freedman, DS and Khan, LK and Dietz, WH and Srinivasan, SR and Berenson, GS},
doi = {10.1542/peds.108.3.712},
file = {:home/riku/Documents/Mendeley Desktop/Freedman et al/Freedman et al.{\_}2001{\_}Relationship of childhood obesity to coronary heart disease risk factors in adulthood the Bogalusa Heart Study.pdf:pdf},
isbn = {1098-4275},
issn = {1098-4275 (Electronic)},
journal = {Pediatrics},
keywords = {obesity},
mendeley-tags = {obesity},
number = {3},
pages = {712--718},
pmid = {11533341},
title = {{Relationship of childhood obesity to coronary heart disease risk factors in adulthood: the Bogalusa Heart Study.}},
volume = {108},
year = {2001}
}
@article{Farooqi2003,
author = {Farooqi, I. Sadaf and Keogh, Julia M. and Yeo, Giles S. H. and Lank, Emma J. and Cheetham, Tim and O'Rahilly, Stephen},
doi = {10.1056/NEJMoa0810625)},
file = {:home/riku/Documents/Mendeley Desktop/Farooqi et al/Farooqi et al.{\_}2003{\_}Clinical spectrum of obesity and mutations in the melanocortin 4 receptor gene.pdf:pdf},
journal = {N. Engl. J. Med.},
keywords = {obesity},
mendeley-tags = {obesity},
number = {12},
pages = {1085--1095},
title = {{Clinical spectrum of obesity and mutations in the melanocortin 4 receptor gene}},
volume = {348},
year = {2003}
}
@article{Waalen2014,
abstract = {The heritability of obesity has long been appreciated and the genetics of obesity has been the focus of intensive study for decades. Early studies elucidating genetic factors involved in rare monogenic and syndromic forms of extreme obesity focused attention on dysfunction of hypothalamic leptin-related pathways in the control of food intake as a major contributor. Subsequent genome-wide association studies of common genetic variants identified novel loci that are involved in more common forms of obesity across populations of diverse ethnicities and ages. The subsequent search for factors contributing to the heritability of obesity not explained by these 2 approaches ("missing heritability") has revealed additional rare variants, copy number variants, and epigenetic changes that contribute. Although clinical applications of these findings have been limited to date, the increasing understanding of the interplay of these genetic factors with environmental conditions, such as the increased availability of high calorie foods and decreased energy expenditure of sedentary lifestyles, promises to accelerate the translation of genetic findings into more successful preventive and therapeutic interventions.},
author = {Waalen, Jill},
doi = {10.1016/j.trsl.2014.05.010},
file = {:home/riku/Documents/Mendeley Desktop/Waalen/Waalen{\_}2014{\_}The genetics of human obesity.pdf:pdf},
isbn = {1931-5244},
issn = {18781810},
journal = {Transl. Res.},
keywords = {BMI = Body mass index,CNV = Copy number variants,CPG = cytosine-phosphate-guanine,GCTA = Genome-wide complex trait analysis,GWAS = Genome-wide association study,ITMAT = Institute for Translational Medicine and T,MAF = Minor allele frequency,PPARG = peroxisome proliferator-activated receptor,SNP = Single-nucleotide polymorphism,WC = waist circumference,WHR = waist-to-hip ratio,obesity},
mendeley-tags = {obesity},
pages = {293--301},
pmid = {24929207},
title = {{The genetics of human obesity}},
volume = {164},
year = {2014}
}
@article{Kanehisa2000,
author = {Kanehisa, Minoru and Goto, Susumu},
doi = {10.1093/nar/27.1.29},
file = {:home/riku/Documents/Mendeley Desktop/Kanehisa, Goto/Kanehisa, Goto{\_}2000{\_}KEGG Kyoto encyclopedia of genes and genomes.pdf:pdf},
isbn = {0305-1048 (Print)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {1},
pages = {27--30},
pmid = {10592173},
title = {{KEGG: Kyoto encyclopedia of genes and genomes}},
volume = {28},
year = {2000}
}
@article{Gilbert2013,
abstract = {Obesity is a problem of epidemic proportions in many developed nations. Increased body mass index and obesity are associated with a significantly worse outcome for many cancers. Breast cancer risk in the postmenopausal setting and poor disease outcome for all patients is significantly augmented in overweight and obese individuals. The expansion of fat tissue involves a complex interaction of endocrine factors known as adipokines and cytokines. High cytokine levels in primary breast cancers and in the circulation of affected patients have been associated with poor outcome. This review summarizes the how cytokine production in obese adipose tissue creates a chronic inflammatory microenvironment that favors tumor cell motility, invasion, and epithelial-mesenchymal transition to enhance the metastatic potential of tumor cells. Many of the cytokines associated with a proinflammatory state are not only upregulated in obese adipose tissue but may also stimulate the self-renewal of cancer stem cells. Thus, enhanced cytokine production in obese adipose tissue may serve both as a chemoattractant for invading cancers and to augment their malignant potential. These new mechanistic insights suggest that the current obesity epidemic will presage a significant increase in cancer incidence, morbidity, and mortality in the next few decades.},
author = {Gilbert, Candace a and Slingerland, Joyce M},
doi = {10.1146/annurev-med-121211-091527},
file = {:home/riku/Documents/Mendeley Desktop/Gilbert, Slingerland/Gilbert, Slingerland{\_}2013{\_}Cytokines, obesity, and cancer new insights on mechanisms linking obesity to cancer risk and progression.pdf:pdf},
isbn = {0066-4219},
issn = {1545-326X},
journal = {Annu. Rev. Med.},
keywords = {Body Mass Index,Cytokines,Cytokines: metabolism,Disease Progression,Humans,Incidence,Neoplasms,Neoplasms: complications,Neoplasms: epidemiology,Neoplasms: metabolism,Obesity,Obesity: complications,Obesity: epidemiology,Obesity: metabolism,Risk Factors,World Health},
number = {October},
pages = {45--57},
pmid = {23121183},
title = {{Cytokines, obesity, and cancer: new insights on mechanisms linking obesity to cancer risk and progression.}},
volume = {64},
year = {2013}
}
@article{Jarde2011,
abstract = {Obesity is associated with an increased risk of breast cancer in postmenopausal women. Accumulating evidence suggests that adipose tissue, which is an endocrine organ producing a large range of factors, may interfere with breast cancer development. Leptin and adiponectin are two major adipocyte-secreted hormones. The pro-carcinogenic effect of leptin and conversely, the anti-carcinogenic effect of adiponectin result from two main mechanisms: a modulation in the signalling pathways involved in proliferation process and a subtle regulation of the apoptotic response. This review provides insight into recent findings on the molecular mechanisms of leptin and adiponectin in mammary tumours, and discusses the potential interplay between these two adipokines in breast cancer.},
author = {Jard{\'{e}}, Thierry and Perrier, St{\'{e}}phane and Vasson, Marie-Paule and Caldefie-Ch{\'{e}}zet, Florence},
doi = {10.1016/j.ejca.2010.09.005},
file = {:home/riku/Documents/Mendeley Desktop/Jard{\'{e}} et al/Jard{\'{e}} et al.{\_}2011{\_}Molecular mechanisms of leptin and adiponectin in breast cancer.pdf:pdf},
isbn = {1879-0852 (Electronic)$\backslash$r0959-8049 (Linking)},
issn = {09598049},
journal = {Eur. J. Cancer},
number = {1},
pages = {33--43},
pmid = {20889333},
title = {{Molecular mechanisms of leptin and adiponectin in breast cancer.}},
volume = {47},
year = {2011}
}
@article{Gelber2008,
abstract = {Objectives: This study examined associations between anthropometric measures (body mass index, waist circumference, waist-to-hip ratio, waist-to-height ratio [WHtR]) and risk of incident cardiovascular disease (CVD) (including nonfatal myocardial infarction, nonfatal ischemic stroke, and cardiovascular death). Background: Controversy exists regarding the optimal approach to measure adiposity, and the utility of body mass index has been questioned. Methods: Participants included 16,332 men in the Physicians' Health Study (mean age 61 years in 1991) and 32,700 women in the Women's Health Study (mean age 61 years in 1999). We used Cox proportional hazards models to determine relative risks and 95{\%} confidence intervals (CIs) for developing CVD according to self-reported anthropometric indexes. Results: A total of 1,505 CVD cases occurred in men and 414 occurred in women (median follow-up 14.2 and 5.5 years, respectively). Although WHtR demonstrated statistically the strongest associations with CVD and best model fit, CVD risk increased linearly and significantly with higher levels of all indexes. Adjusting for confounders, the relative risk for CVD was 0.58 (95{\%} CI: 0.32 to 1.05) for men with the lowest WHtR ({\textless}0.45) and 2.36 (95{\%} CI: 1.61 to 3.47) for the highest WHtR (???0.69; vs. WHtR 0.49 to {\textless}0.53). Among women, the relative risk was 0.65 (95{\%} CI: 0.33 to 1.31) for those with the lowest WHtR ({\textless}0.42) and 2.33 (95{\%} CI: 1.66 to 3.28) for the highest WHtR (???0.68; vs. WHtR 0.47 to {\textless}0.52). Conclusions: The WHtR demonstrated statistically the best model fit and strongest associations with CVD. However, compared with body mass index, differences in cardiovascular risk assessment using other indexes were small and likely not clinically consequential. Our findings emphasize that higher levels of adiposity, however measured, confer increased risk of CVD. ?? 2008 American College of Cardiology Foundation.},
author = {Gelber, Rebecca P. and Gaziano, J. Michael and Orav, E. John and Manson, JoAnn E. and Buring, Julie E. and Kurth, Tobias},
doi = {10.1016/j.jacc.2008.03.066},
file = {:home/riku/Documents/Mendeley Desktop/Gelber et al/Gelber et al.{\_}2008{\_}Measures of Obesity and Cardiovascular Risk Among Men and Women.pdf:pdf},
isbn = {07351097},
issn = {07351097},
journal = {J. Am. Coll. Cardiol.},
keywords = {cardiovascular disease,epidemiology,obesity},
mendeley-tags = {obesity},
number = {8},
pages = {605--615},
pmid = {18702962},
publisher = {Elsevier Masson SAS},
title = {{Measures of Obesity and Cardiovascular Risk Among Men and Women}},
volume = {52},
year = {2008}
}
@article{Lawrence2013,
abstract = {Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.},
author = {Lawrence, Michael S and Stojanov, Petar and Polak, Paz and Kryukov, Gregory V and Cibulskis, Kristian and Sivachenko, Andrey and Carter, Scott L and Stewart, Chip and Mermel, Craig H and Roberts, Steven A and Kiezun, Adam and Hammerman, Peter S and McKenna, Aaron and Drier, Yotam and Zou, Lihua and Ramos, Alex H and Pugh, Trevor J and Stransky, Nicolas and Helman, Elena and Kim, Jaegil and Sougnez, Carrie and Ambrogio, Lauren and Nickerson, Elizabeth and Shefler, Erica and Cort{\'{e}}s, Maria L and Auclair, Daniel and Saksena, Gordon and Voet, Douglas and Noble, Michael and DiCara, Daniel and Lin, Pei and Lichtenstein, Lee and Heiman, David I and Fennell, Timothy and Imielinski, Marcin and Hernandez, Bryan and Hodis, Eran and Baca, Sylvan and Dulak, Austin M and Lohr, Jens and Landau, Dan-Avi and Wu, Catherine J and Melendez-Zajgla, Jorge and Hidalgo-Miranda, Alfredo and Koren, Amnon and McCarroll, Steven A and Mora, Jaume and Lee, Ryan S and Crompton, Brian and Onofrio, Robert and Parkin, Melissa and Winckler, Wendy and Ardlie, Kristin and Gabriel, Stacey B and Roberts, Charles W M and Biegel, Jaclyn A and Stegmaier, Kimberly and Bass, Adam J and Garraway, Levi A and Meyerson, Matthew and Golub, Todd R and Gordenin, Dmitry A and Sunyaev, Shamil and Lander, Eric S and Getz, Gad},
doi = {10.1038/nature12213},
file = {:home/riku/Documents/Mendeley Desktop/Lawrence et al/Lawrence et al.{\_}2013{\_}Mutational heterogeneity in cancer and the search for new cancer-associated genes.pdf:pdf},
isbn = {1476-4687 (Electronic)$\backslash$r0028-0836 (Linking)},
issn = {1476-4687},
journal = {Nature},
keywords = {Artifacts,DNA Replication Timing,Exome,Exome: genetics,False Positive Reactions,Gene Expression,Genetic Heterogeneity,Genome,Human,Human: genetics,Humans,Lung Neoplasms,Lung Neoplasms: genetics,Mutation,Mutation Rate,Mutation: genetics,Neoplasms,Neoplasms: classification,Neoplasms: genetics,Neoplasms: pathology,Oncogenes,Oncogenes: genetics,Reproducibility of Results,Sample Size,Squamous Cell,Squamous Cell: genetics},
number = {7457},
pages = {214--218},
pmid = {23770567},
title = {{Mutational heterogeneity in cancer and the search for new cancer-associated genes.}},
volume = {499},
year = {2013}
}
@article{Mckeown1994,
author = {McKeown-Eyssen, Gail},
file = {:home/riku/Documents/Mendeley Desktop/McKeown-Eyssen/McKeown-Eyssen{\_}1994{\_}Epidemiology Triglycerides of Colorectal and or Plasma Cancer Glucose Revisited Associated Are Serum with Risk.pdf:pdf},
journal = {Cancer Epidemiol. Biomarkers Prev.},
keywords = {insulin cancer hypothesis},
mendeley-tags = {insulin cancer hypothesis},
number = {December},
pages = {687-- 695},
title = {{Epidemiology Triglycerides of Colorectal and / or Plasma Cancer Glucose Revisited : Associated Are Serum with Risk ?}},
volume = {3},
year = {1994}
}
@article{Khatri2012,
abstract = {Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces complexity and has increased explanatory power. We discuss the evolution of knowledge base-driven pathway analysis over its first decade, distinctly divided into three generations. We also discuss the limitations that are specific to each generation, and how they are addressed by successive generations of methods. We identify a number of annotation challenges that must be addressed to enable development of the next generation of pathway analysis methods. Furthermore, we identify a number of methodological challenges that the next generation of methods must tackle to take advantage of the technological advances in genomics and proteomics in order to improve specificity, sensitivity, and relevance of pathway analysis.},
author = {Khatri, Purvesh and Sirota, Marina and Butte, Atul J.},
doi = {10.1371/journal.pcbi.1002375},
file = {:home/riku/Documents/Mendeley Desktop/Khatri, Sirota, Butte/Khatri, Sirota, Butte{\_}2012{\_}Ten years of pathway analysis Current approaches and outstanding challenges.PDF:PDF},
isbn = {1553-7358 (Electronic)$\backslash$r1553-734X (Linking)},
issn = {1553734X},
journal = {PLoS Comput. Biol.},
number = {2},
pmid = {22383865},
title = {{Ten years of pathway analysis: Current approaches and outstanding challenges}},
volume = {8},
year = {2012}
}
@article{Alexandrov2013,
abstract = {All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.},
author = {Alexandrov, Ludmil B and Nik-Zainal, Serena and Wedge, David C and Aparicio, Samuel A J R and Behjati, Sam and Biankin, Andrew V and Bignell, Graham R and Bolli, Niccol{\`{o}} and Borg, Ake and B{\o}rresen-Dale, Anne-Lise and Boyault, Sandrine and Burkhardt, Birgit and Butler, Adam P and Caldas, Carlos and Davies, Helen R and Desmedt, Christine and Eils, Roland and Eyfj{\"{o}}rd, J{\'{o}}runn Erla and Foekens, John a and Greaves, Mel and Hosoda, Fumie and Hutter, Barbara and Ilicic, Tomislav and Imbeaud, Sandrine and Imielinski, Marcin and Imielinsk, Marcin and J{\"{a}}ger, Natalie and Jones, David T W and Jones, David and Knappskog, Stian and Kool, Marcel and Lakhani, Sunil R and L{\'{o}}pez-Ot{\'{i}}n, Carlos and Martin, Sancha and Munshi, Nikhil C and Nakamura, Hiromi and Northcott, Paul a and Pajic, Marina and Papaemmanuil, Elli and Paradiso, Angelo and Pearson, John V and Puente, Xose S and Raine, Keiran and Ramakrishna, Manasa and Richardson, Andrea L and Richter, Julia and Rosenstiel, Philip and Schlesner, Matthias and Schumacher, Ton N and Span, Paul N and Teague, Jon W and Totoki, Yasushi and Tutt, Andrew N J and Vald{\'{e}}s-Mas, Rafael and van Buuren, Marit M and {van 't Veer}, Laura and Vincent-Salomon, Anne and Waddell, Nicola and Yates, Lucy R and Zucman-Rossi, Jessica and Futreal, P Andrew and McDermott, Ultan and Lichter, Peter and Meyerson, Matthew and Grimmond, Sean M and Siebert, Reiner and Campo, El{\'{i}}as and Shibata, Tatsuhiro and Pfister, Stefan M and Campbell, Peter J and Stratton, Michael R},
doi = {10.1038/nature12477},
file = {:home/riku/Documents/Mendeley Desktop/Alexandrov et al/Alexandrov et al.{\_}2013{\_}Signatures of mutational processes in human cancer.pdf:pdf},
isbn = {1476-4687 (Electronic)$\backslash$r0028-0836 (Linking)},
issn = {1476-4687},
journal = {Nature},
keywords = {Aging,Aging: genetics,Algorithms,Cell Transformation,Cytidine Deaminase,Cytidine Deaminase: genetics,DNA,DNA Mutational Analysis,DNA: genetics,DNA: metabolism,Genetic,Genetic: genetics,Humans,Insertional,Insertional: genetics,Models,Mutagenesis,Mutagenesis: genetics,Mutagens,Mutagens: pharmacology,Mutation,Mutation: genetics,Neoplasms,Neoplasms: enzymology,Neoplasms: genetics,Neoplasms: pathology,Neoplastic,Neoplastic: genetics,Neoplastic: pathology,Organ Specificity,Reproducibility of Results,Sequence Deletion,Sequence Deletion: genetics,Transcription},
number = {7463},
pages = {415--421},
pmid = {23945592},
title = {{Signatures of mutational processes in human cancer.}},
volume = {500},
year = {2013}
}
@article{Lim2012,
abstract = {Background Quantification of the disease burden caused by different risks informs prevention by providing an account of health loss different to that provided by a disease-by-disease analysis. No complete revision of global disease burden caused by risk factors has been done since a comparative risk assessment in 2000, and no previous analysis has assessed changes in burden attributable to risk factors over time. Methods We estimated deaths and disability-adjusted life years; DALYs; sum of years lived with disability [YLD] and years of life lost [YLL]) attributable to the independent effects of 67 risk factors and clusters of risk factors for 21 regions in 1990 and 2010. We estimated exposure distributions for each year, region, sex, and age group, and relative risks per unit of exposure by systematically reviewing and synthesising published and unpublished data. We used these estimates, together with estimates of cause-specific deaths and DALYs from the Global Burden of Disease Study 2010, to calculate the burden attributable to each risk factor exposure compared with the theoretical-minimum-risk exposure. We incorporated uncertainty in disease burden, relative risks, and exposures into our estimates of attributable burden. Findings In 2010, the three leading risk factors for global disease burden were high blood pressure (7 0{\%} [95{\%} uncertainty interval 6 2-7 7] of global DALYs); tobacco smoking including second-hand smoke (6 3{\%} [5 5-7 0]), and alcohol use (5 5{\%} [5 0-5 9]). In 1990, the leading risks were childhood underweight (7 9{\%} [6 8-9 4]), household air pollution from solid fuels; (HAP; 7 0{\%} [5 6-8 3]), and tobacco smoking including second-hand smoke (6 1{\%} [5 4-6 8]). Dietary risk factors and physical inactivity collectively accounted for 10 0{\%} (95{\%} UI 9 2-10 8) of global DALYs in 2010, with the most prominent dietary risks being diets low in fruits and those high in sodium. Several risks that primarily affect childhood communicable diseases, including unimproved water and sanitation and childhood micronutrient deficiencies, fell in rank between 1990 and 2010, with unimproved water ' and sanitation accounting for 0 9{\%} (0 4-1 6) of global DALYs in 2010. However, in most of sub-Saharan Africa childhood underweight, HAP, and non-exclusive and discontinued breastfeeding were the leading risks in 2010, while HAP was the leading risk in south Asia. The leading risk factor in Eastern Europe, most of Latin America, and southern sub-Saharan Africa in 2010 was alcohol use; in most of Asia, North Africa and Middle East, and central Europe it was high blood pressure. Despite declines, tobacco smoking including second-hand smoke remained the leading risk in high-income north America and western Europe. High body-mass index has increased globally and it is the leading risk in Australasia and southern Latin America, and also ranks high in other high-income regions, North Africa and Middle East, and Oceania. Interpretation Worldwide, the contribution of different risk factors to disease burden has changed substantially, with a shift away from risks for communicable diseases in children towards those for non-communicable diseases in adults. These changes are related to the ageing population, decreased mortality among children younger than 5 years, changes in cause-of-death composition, and changes in risk factor exposures. New evidence has led to changes in the magnitude of key risks including unimproved water and sanitation, vitamin A and zinc deficiencies, and ambient particulate matter pollution. The extent to which the epidemiological shift has occurred and what the leading risks currently are varies greatly across regions. In much of sub-Saharan Africa, the leading risks are still those associated with poverty and those that affect children.},
author = {Lim, Stephen S. and Vos, Theo and Flaxman, Abraham D. and Danaei, Goodarz and Shibuya, Kenji and Adair-Rohani, Heather and Amann, Markus and Anderson, H. Ross and Andrews, Kathryn G. and Aryee, Martin and Atkinson, Charles and Bacchus, Loraine J. and Bahalim, Adil N. and Balakrishnan, Kalpana and Balmes, John and Barker-Collo, Suzanne and Baxter, Amanda and Bell, Michelle L. and Blore, Jed D. and Blyth, Fiona and Bonner, Carissa and Borges, Guilherme and Bourne, Rupert and Boussinesq, Michel and Brauer, Michael and Brooks, Peter and Bruce, Nigel G. and Brunekreef, Bert and Bryan-Hancock, Claire and Bucello, Chiara and Buchbinder, Rachelle and Bull, Fiona and Burnett, Richard T. and Byers, Tim E. and Calabria, Bianca and Carapetis, Jonathan and Carnahan, Emily and Chafe, Zoe and Charlson, Fiona and Chen, Honglei and Chen, Jian Shen and Cheng, Andrew Tai Ann and Child, Jennifer Christine and Cohen, Aaron and Colson, K. Ellicott and Cowie, Benjamin C. and Darby, Sarah and Darling, Susan and Davis, Adrian and Degenhardt, Louisa and Dentener, Frank and {Des Jarlais}, Don C. and Devries, Karen and Dherani, Mukesh and Ding, Eric L. and Dorsey, E. Ray and Driscoll, Tim and Edmond, Karen and Ali, Suad Eltahir and Engell, Rebecca E. and Erwin, Patricia J. and Fahimi, Saman and Falder, Gail and Farzadfar, Farshad and Ferrari, Alize and Finucane, Mariel M. and Flaxman, Seth and Fowkes, Francis Gerry R and Freedman, Greg and Freeman, Michael K. and Gakidou, Emmanuela and Ghosh, Santu and Giovannucci, Edward and Gmel, Gerhard and Graham, Kathryn and Grainger, Rebecca and Grant, Bridget and Gunnell, David and Gutierrez, Hialy R. and Hall, Wayne and Hoek, Hans W. and Hogan, Anthony and Hosgood, H. Dean and Hoy, Damian and Hu, Howard and Hubbell, Bryan J. and Hutchings, Sally J. and Ibeanusi, Sydney E. and Jacklyn, Gemma L. and Jasrasaria, Rashmi and Jonas, Jost B. and Kan, Haidong and Kanis, John A. and Kassebaum, Nicholas and Kawakami, Norito and Khang, Young Ho and Khatibzadeh, Shahab and Khoo, Jon Paul and Kok, Cindy and Laden, Francine and Lalloo, Ratilal and Lan, Qing and Lathlean, Tim and Leasher, Janet L. and Leigh, James and Li, Yang and Lin, John Kent and Lipshultz, Steven E. and London, Stephanie and Lozano, Rafael and Lu, Yuan and Mak, Joelle and Malekzadeh, Reza and Mallinger, Leslie and Marcenes, Wagner and March, Lyn and Marks, Robin and Martin, Randall and McGale, Paul and McGrath, John and Mehta, Sumi and Mensah, George A. and Merriman, Tony R. and Micha, Renata and Michaud, Catherine and Mishra, Vinod and Hanafiah, Khayriyyah Mohd and Mokdad, Ali A. and Morawska, Lidia and Mozaffarian, Dariush and Murphy, Tasha and Naghavi, Mohsen and Neal, Bruce and Nelson, Paul K. and Nolla, Joan Miquel and Norman, Rosana and Olives, Casey and Omer, Saad B. and Orchard, Jessica and Osborne, Richard and Ostro, Bart and Page, Andrew and Pandey, Kiran D. and Parry, Charles D H and Passmore, Erin and Patra, Jayadeep and Pearce, Neil and Pelizzari, Pamela M. and Petzold, Max and Phillips, Michael R. and Pope, Dan and Pope, C. Arden and Powles, John and Rao, Mayuree and Razavi, Homie and Rehfuess, Eva A. and Rehm, J{\"{u}}rgen T. and Ritz, Beate and Rivara, Frederick P. and Roberts, Thomas and Robinson, Carolyn and Rodriguez-Portales, Jose A. and Romieu, Isabelle and Room, Robin and Rosenfeld, Lisa C. and Roy, Ananya and Rushton, Lesley and Salomon, Joshua A. and Sampson, Uchechukwu and Sanchez-Riera, Lidia and Sanman, Ella and Sapkota, Amir and Seedat, Soraya and Shi, Peilin and Shield, Kevin and Shivakoti, Rupak and Singh, Gitanjali M. and Sleet, David A. and Smith, Emma and Smith, Kirk R. and Stapelberg, Nicolas J C and Steenland, Kyle and St{\"{o}}ckl, Heidi and Stovner, Lars Jacob and Straif, Kurt and Straney, Lahn and Thurston, George D. and Tran, Jimmy H. and {Van Dingenen}, Rita and {Van Donkelaar}, Aaron and Veerman, J. Lennert and Vijayakumar, Lakshmi and Weintraub, Robert and Weissman, Myrna M. and White, Richard A. and Whiteford, Harvey and Wiersma, Steven T. and Wilkinson, James D. and Williams, Hywel C. and Williams, Warwick and Wilson, Nicholas and Woolf, Anthony D. and Yip, Paul and Zielinski, Jan M. and Lopez, Alan D. and Murray, Christopher J L and Ezzati, Majid},
doi = {10.1016/S0140-6736(12)61766-8},
file = {:home/riku/Documents/Mendeley Desktop/Lim et al/Lim et al.{\_}2012{\_}A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters i.pdf:pdf},
isbn = {0140-6736},
issn = {01406736},
journal = {Lancet},
keywords = {obesity},
mendeley-tags = {obesity},
number = {9859},
pages = {2224--2260},
pmid = {23245609},
title = {{A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990-2010: A systematic analysis for the Global Burden of Disease Study 2010}},
volume = {380},
year = {2012}
}
@article{Chang2013,
abstract = {The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.},
author = {Chang, Kyle and Creighton, Chad J and Davis, Caleb and Donehower, Lawrence and Drummond, Jennifer and Wheeler, David and Ally, Adrian and Balasundaram, Miruna and Birol, Inanc and Butterfield, Yaron S N and Chu, Andy and Chuah, Eric and Chun, Hye-Jung E and Dhalla, Noreen and Guin, Ranabir and Hirst, Martin and Hirst, Carrie and Holt, Robert A and Jones, Steven J M and Lee, Darlene and Li, Haiyan I and Marra, Marco A and Mayo, Michael and Moore, Richard A and Mungall, Andrew J and Robertson, A Gordon and Schein, Jacqueline E and Sipahimalani, Payal and Tam, Angela and Thiessen, Nina and Varhol, Richard J and Beroukhim, Rameen and Bhatt, Ami S and Brooks, Angela N and Cherniack, Andrew D and Freeman, Samuel S and Gabriel, Stacey B and Helman, Elena and Jung, Joonil and Meyerson, Matthew and Ojesina, Akinyemi I and Pedamallu, Chandra Sekhar and Saksena, Gordon and Schumacher, Steven E and Tabak, Barbara and Zack, Travis and Lander, Eric S and Bristow, Christopher A and Hadjipanayis, Angela and Haseley, Psalm and Kucherlapati, Raju and Lee, Semin and Lee, Eunjung and Luquette, Lovelace J and Mahadeshwar, Harshad S and Pantazi, Angeliki and Parfenov, Michael and Park, Peter J and Protopopov, Alexei and Ren, Xiaojia and Santoso, Netty and Seidman, Jonathan and Seth, Sahil and Song, Xingzhi and Tang, Jiabin and Xi, Ruibin and Xu, Andrew W and Yang, Lixing and Zeng, Dong and Auman, J Todd and Balu, Saianand and Buda, Elizabeth and Fan, Cheng and Hoadley, Katherine A and Jones, Corbin D and Meng, Shaowu and Mieczkowski, Piotr A and Parker, Joel S and Perou, Charles M and Roach, Jeffrey and Shi, Yan and Silva, Grace O and Tan, Donghui and Veluvolu, Umadevi and Waring, Scot and Wilkerson, Matthew D and Wu, Junyuan and Zhao, Wei and Bodenheimer, Tom and Hayes, D Neil and Hoyle, Alan P and Jeffreys, Stuart R and Mose, Lisle E and Simons, Janae V and Soloway, Mathew G and Baylin, Stephen B and Berman, Benjamin P and Bootwalla, Moiz S and Danilova, Ludmila and Herman, James G and Hinoue, Toshinori and Laird, Peter W and Rhie, Suhn K and Shen, Hui and Triche, Timothy and Weisenberger, Daniel J and Carter, Scott L and Cibulskis, Kristian and Chin, Lynda and Zhang, Jianhua and Getz, Gad and Sougnez, Carrie and Wang, Min and Dinh, Huyen and Doddapaneni, Harsha Vardhan and Gibbs, Richard and Gunaratne, Preethi and Han, Yi and Kalra, Divya and Kovar, Christie and Lewis, Lora and Morgan, Margaret and Morton, Donna and Muzny, Donna and Reid, Jeffrey and Xi, Liu and Cho, Juok and Dicara, Daniel and Frazer, Scott and Gehlenborg, Nils and Heiman, David I and Kim, Jaegil and Lawrence, Michael S and Lin, Pei and Liu, Yingchun and Noble, Michael S and Stojanov, Petar and Voet, Doug and Zhang, Hailei and Zou, Lihua and Stewart, Chip and Bernard, Brady and Bressler, Ryan and Eakin, Andrea and Iype, Lisa and Knijnenburg, Theo and Kramer, Roger and Kreisberg, Richard and Leinonen, Kalle and Lin, Jake and Liu, Yuexin and Miller, Michael and Reynolds, Sheila M and Rovira, Hector and Shmulevich, Ilya and Thorsson, Vesteinn and Yang, Da and Zhang, Wei and Amin, Samirkumar and Wu, Chang-Jiun and Wu, Chia-Chin and Akbani, Rehan and Aldape, Kenneth and Baggerly, Keith A and Broom, Bradley and Casasent, Tod D and Cleland, James and Creighton, Chad and Dodda, Deepti and Edgerton, Mary and Han, Leng and Herbrich, Shelley M and Ju, Zhenlin and Kim, Hoon and Lerner, Seth and Li, Jun and Liang, Han and Liu, Wenbin and Lorenzi, Philip L and Lu, Yiling and Melott, James and Mills, Gordon B and Nguyen, Lam and Su, Xiaoping and Verhaak, Roeland and Wang, Wenyi and Weinstein, John N and Wong, Andrew and Yang, Yang and Yao, Jun and Yao, Rong and Yoshihara, Kosuke and Yuan, Yuan and Yung, Alfred K and Zhang, Nianxiang and Zheng, Siyuan and Ryan, Michael and Kane, David W and Aksoy, B Arman and Ciriello, Giovanni and Dresdner, Gideon and Gao, Jianjiong and Gross, Benjamin and Jacobsen, Anders and Kahles, Andre and Ladanyi, Marc and Lee, William and Lehmann, Kjong-Van and Miller, Martin L and Ramirez, Ricardo and R{\"{a}}tsch, Gunnar and Reva, Boris and Sander, Chris and Schultz, Nikolaus and Senbabaoglu, Yasin and Shen, Ronglai and Sinha, Rileen and Sumer, S Onur and Sun, Yichao and Taylor, Barry S and Weinhold, Nils and Fei, Suzanne and Spellman, Paul and Benz, Christopher and Carlin, Daniel and Cline, Melisssa and Craft, Brian and Ellrott, Kyle and Goldman, Mary and Haussler, David and Ma, Singer and Ng, Sam and Paull, Evan and Radenbaugh, Amie and Salama, Sofie and Sokolov, Artem and Stuart, Joshua M and Swatloski, Teresa and Uzunangelov, Vladislav and Waltman, Peter and Yau, Christina and Zhu, Jing and Hamilton, Stanley R and Abbott, Scott and Abbott, Rachel and Dees, Nathan D and Delehaunty, Kim and Ding, Li and Dooling, David J and Eldred, Jim M and Fronick, Catrina C and Fulton, Robert and Fulton, Lucinda L and Kalicki-Veizer, Joelle and Kanchi, Krishna-Latha and Kandoth, Cyriac and Koboldt, Daniel C and Larson, David E and Ley, Timothy J and Lin, Ling and Lu, Charles and Magrini, Vincent J and Mardis, Elaine R and McLellan, Michael D and McMichael, Joshua F and Miller, Christopher A and O'Laughlin, Michelle and Pohl, Craig and Schmidt, Heather and Smith, Scott M and Walker, Jason and Wallis, John W and Wendl, Michael C and Wilson, Richard K and Wylie, Todd and Zhang, Qunyuan and Burton, Robert and Jensen, Mark A and Kahn, Ari and Pihl, Todd and Pot, David and Wan, Yunhu and Levine, Douglas A and Black, Aaron D and Bowen, Jay and Frick, Jessica and Gastier-Foster, Julie M and Harper, Hollie A and Helsel, Carmen and Leraas, Kristen M and Lichtenberg, Tara M and McAllister, Cynthia and Ramirez, Nilsa C and Sharpe, Samantha and Wise, Lisa and Zmuda, Erik and Chanock, Stephen J and Davidsen, Tanja and Demchok, John A and Eley, Greg and Felau, Ina and Ozenberger, Brad A and Sheth, Margi and Sofia, Heidi and Staudt, Louis and Tarnuzzer, Roy and Wang, Zhining and Yang, Liming and Zhang, Jiashan and Omberg, Larsson and Margolin, Adam and Raphael, Benjamin J and Vandin, Fabio and Wu, Hsin-Ta and Leiserson, Mark D M and Benz, Stephen C and Vaske, Charles J and Noushmehr, Houtan and Wolf, Denise and Veer, Laura Van't and Collisson, Eric A and Anastassiou, Dimitris and {Ou Yang}, Tai-Hsien and Lopez-Bigas, Nuria and Gonzalez-Perez, Abel and Tamborero, David and Xia, Zheng and Li, Wei and Cho, Dong-Yeon and Przytycka, Teresa and Hamilton, Mark and McGuire, Sean and Nelander, Sven and Johansson, Patrik and J{\"{o}}rnsten, Rebecka and Kling, Teresia and Sanchez, Jose and Shaw, Kenna R Mills},
doi = {10.1038/ng.2764},
file = {:home/riku/Documents/Mendeley Desktop/Chang et al/Chang et al.{\_}2013{\_}The Cancer Genome Atlas Pan-Cancer analysis project.pdf:pdf},
isbn = {doi:10.1038/ng.2764},
issn = {1546-1718},
journal = {Nat. Genet.},
number = {10},
pages = {1113--1120},
pmid = {24071849},
publisher = {Nature Publishing Group},
title = {{The Cancer Genome Atlas Pan-Cancer analysis project.}},
volume = {45},
year = {2013}
}
@article{Montague1997,
abstract = {The extreme obesity of the obese (ob/ob) mouse is attributable to mutations in the gene encoding leptin, an adipocyte-specific secreted protein which has profound effects on appetite and energy expenditure. We know of no equivalent evidence regarding leptin's role in the control of fat mass in humans. We have examined two severely obese children who are members of the same highly consanguineous pedigree. Their serum leptin levels were very low despite their markedly elevated fat mass and, in both, a homozygous frame-shift mutation involving the deletion of a single guanine nucleotide in codon 133 of the gene for leptin was found. The severe obesity found in these congenitally leptin-deficient subjects provides the first genetic evidence that leptin is an important regulator of energy balance in humans.},
author = {Montague, C T and Farooqi, I S and Whitehead, J P and Soos, M a and Rau, H and Wareham, N J and Sewter, C P and Digby, J E and Mohammed, S N and Hurst, J a and Cheetham, C H and Earley, a R and Barnett, a H and Prins, J B and O'Rahilly, S},
doi = {10.1038/43185},
file = {:home/riku/Documents/Mendeley Desktop/Montague et al/Montague et al.{\_}1997{\_}Congenital leptin deficiency is associated with severe early-onset obesity in humans.pdf:pdf},
isbn = {0028-0836 (Print)},
issn = {0028-0836},
journal = {Nature},
keywords = {obesity},
mendeley-tags = {obesity},
number = {6636},
pages = {903--908},
pmid = {9202122},
title = {{Congenital leptin deficiency is associated with severe early-onset obesity in humans.}},
volume = {387},
year = {1997}
}
@article{Jackson1997,
author = {Jackson, Robert S. and Creemers, John W M and Ohagi, Shinya and Raffin-Sanson, Marie-Laure and Sanders, Louise and Montague, Carl T and Hutton, John C. and O'Rahilly, Stephen},
file = {:home/riku/Documents/Mendeley Desktop/Jackson et al/Jackson et al.{\_}1997{\_}Obesity and impaired prohormone processing associated with mutations in the human prohormone convertase 1 gene.pdf:pdf},
journal = {Nat. Genet.},
keywords = {obesity},
mendeley-tags = {obesity},
pages = {303--306},
pmid = {8985244},
title = {{Obesity and impaired prohormone processing associated with mutations in the human prohormone convertase 1 gene}},
volume = {16},
year = {1997}
}
@article{Lagergren1999,
author = {Lagergren, Jesper},
doi = {10.7326/0003-4819-130-11-199906010-00003},
file = {:home/riku/Documents/Mendeley Desktop/Lagergren/Lagergren{\_}1999{\_}Association between Body Mass and Adenocarcinoma of the Esophagus and Gastric Cardia.pdf:pdf},
issn = {0003-4819},
journal = {Ann. Intern. Med.},
month = {jun},
number = {11},
pages = {883--890},
publisher = {American College of Physicians},
title = {{Association between Body Mass and Adenocarcinoma of the Esophagus and Gastric Cardia}},
volume = {130},
year = {1999}
}
@article{Saxena2006,
abstract = {Obesity, as a core component of the metabolic syndrome, is among the top ten global health risks classified by the World Health Organization (WHO) as being strongly associated with the development and progression of chronic renal disease--a widely prevalent but often silent condition. Obesity carries elevated risks of cardiovascular morbidity and mortality besides having an array of metabolic complications. Maladaptive glomerular hemodynamics with increased intraglomerular pressure in association with vasoactive, fibrogenic substances released from adipocytes, in addition to cytokines and hormones, are the key factors in the causation of renal injury and the progression of nephron loss among obese subjects.},
author = {Saxena, Anil Kumar},
doi = {10.1093/epirev/mxm012},
file = {:home/riku/Documents/Mendeley Desktop/Saxena/Saxena{\_}2006{\_}Emerging global epidemic of obesity The renal perspective.pdf:pdf},
isbn = {0256-4947 (Print)$\backslash$n0256-4947 (Linking)},
issn = {02564947},
journal = {Ann. Saudi Med.},
keywords = {obesity},
mendeley-tags = {obesity},
number = {4},
pages = {288--295},
pmid = {16883080},
title = {{Emerging global epidemic of obesity: The renal perspective}},
volume = {26},
year = {2006}
}
@article{Huang2009,
abstract = {Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.},
author = {Huang, Da Wei and Sherman, Brad T. and Lempicki, Richard A.},
doi = {10.1093/nar/gkn923},
file = {:home/riku/Documents/Mendeley Desktop/Huang, Sherman, Lempicki/Huang, Sherman, Lempicki{\_}2009{\_}Bioinformatics enrichment tools Paths toward the comprehensive functional analysis of large gene lists.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {1},
pages = {1--13},
pmid = {19033363},
title = {{Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists}},
volume = {37},
year = {2009}
}
@article{Goeman2007,
abstract = {Motivation: Many statistical tests have been proposed in recent years for analyzing gene expression data in terms of gene sets, usually from Gene Ontology. These methods are based on widely different methodological assumptions. Some approaches test differential expression of each gene set against differential expression of the rest of the genes, whereas others test each gene set on its own. Also, some methods are based on a model in which the genes are the sampling units, whereas others treat the subjects as the sampling units. This article aims to clarify the assumptions behind different approaches and to indicate a preferential methodology of gene set testing.$\backslash$nResults: We identify some crucial assumptions which are needed by the majority of methods. P-values derived from methods that use a model which takes the genes as the sampling unit are easily misinterpreted, as they are based on a statistical model that does not resemble the biological experiment actually performed. Furthermore, because these models are based on a crucial and unrealistic independence assumption between genes, the P-values derived from such methods can be wildly anti-conservative, as a simulation experiment shows. We also argue that methods that competitively test each gene set against the rest of the genes create an unnecessary rift between single gene testing and gene set testing.$\backslash$nContact: j.j.goeman@lumc.nl},
author = {Goeman, Jelle J. and B{\"{u}}hlmann, Peter},
doi = {10.1093/bioinformatics/btm051},
file = {:home/riku/Documents/Mendeley Desktop/Goeman, B{\"{u}}hlmann/Goeman, B{\"{u}}hlmann{\_}2007{\_}Analyzing gene expression data in terms of gene sets Methodological issues.pdf:pdf},
isbn = {1367-4811 (Electronic)$\backslash$r1367-4803 (Linking)},
issn = {13674803},
journal = {Bioinformatics},
number = {8},
pages = {980--987},
pmid = {17303618},
title = {{Analyzing gene expression data in terms of gene sets: Methodological issues}},
volume = {23},
year = {2007}
}
@article{Tarca2013,
abstract = {Identification of functional sets of genes associated with conditions of interest from omics data was first reported in 1999, and since, a plethora of enrichment methods were published for systematic analysis of gene sets collections including Gene Ontology and biological pathways. Despite their widespread usage in reducing the complexity of omics experiment results, their performance is poorly understood. Leveraging the existence of disease specific gene sets in KEGG and Metacore{\textregistered} databases, we compared the performance of sixteen methods under relaxed assumptions while using 42 real datasets (over 1,400 samples). Most of the methods ranked high the gene sets designed for specific diseases whenever samples from affected individuals were compared against controls via microarrays. The top methods for gene set prioritization were different from the top ones in terms of sensitivity, and four of the sixteen methods had large false positives rates assessed by permuting the phenotype of the samples. The best overall methods among those that generated reasonably low false positive rates, when permuting phenotypes, were PLAGE, GLOBALTEST, and PADOG. The best method in the category that generated higher than expected false positives was MRGSE.},
author = {Tarca, Adi L. and Bhatti, Gaurav and Romero, Roberto},
doi = {10.1371/journal.pone.0079217},
file = {:home/riku/Documents/Mendeley Desktop/Tarca, Bhatti, Romero/Tarca, Bhatti, Romero{\_}2013{\_}A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity.pdf:pdf},
isbn = {1932-6203},
issn = {19326203},
journal = {PLoS One},
number = {11},
pages = {e79217},
pmid = {24260172},
title = {{A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity}},
volume = {8},
year = {2013}
}
@article{Hurd2009,
abstract = {Several recent studies from the field of epigenetics have combined chromatin-immunoprecipitation (ChIP) with next-generation high-throughput sequencing technologies to describe the locations of histone post-translational modifications (PTM) and DNA methylation genome-wide. While these reports begin to quench the chromatin biologists thirst for visualizing where in the genome epigenetic marks are placed, they also illustrate several advantages of sequencing based genomics compared to microarray analysis. Accordingly, next-generation sequencing (NGS) technologies are now challenging microarrays as the tool of choice for genome analysis. The increased affordability of comprehensive sequence-based genomic analysis will enable new questions to be addressed in many areas of biology. It is inevitable that massively-parallel sequencing platforms will supercede the microarray for many applications, however, there are niches for microarrays to fill and interestingly we may very well witness a symbiotic relationship between microarrays and high-throughput sequencing in the future.},
author = {Hurd, Paul J. and Nelson, Christopher J.},
doi = {10.1093/bfgp/elp013},
file = {:home/riku/Documents/Mendeley Desktop/Hurd, Nelson/Hurd, Nelson{\_}2009{\_}Advantages of next-generation sequencing versus the microarray in epigenetic research.pdf:pdf},
isbn = {1477-4062 (Electronic)$\backslash$r1473-9550 (Linking)},
issn = {14739550},
journal = {Briefings Funct. Genomics Proteomics},
keywords = {ABI SOLiD,ChIP-Seq,Microarray,Next-generation sequencing,Roche 454 pyrosequencing,Solexa/Illumina},
number = {3},
pages = {174--183},
pmid = {19535508},
title = {{Advantages of next-generation sequencing versus the microarray in epigenetic research}},
volume = {8},
year = {2009}
}
@article{Pate1995,
author = {Pate, Russell R and Pratt, Michael and Blair, Steven N and Haskell, William L and Macera, Caroline A and Bouchard, Claude and Buchner, David and Ettinger, Walter and Heath, Gregory W and King, Abby C and Kriska, Andrea and Leon, Arthur S and Marcus, Bess H and Morris, Jeremy and Paffenbarger, Ralph S and Patrick, Kevin and Pollock, Michael L and Rippe, James M and Sallis, James and Wilmore, Jack H},
file = {:home/riku/Documents/Mendeley Desktop/Pate et al/Pate et al.{\_}1995{\_}Physical activity and public health A recommendation from the Centers for Disease Control and prevention and the Americ.pdf:pdf},
journal = {J. Am. Med. Assoc.},
keywords = {obesity},
mendeley-tags = {obesity},
number = {5},
pages = {402--407},
title = {{Physical activity and public health: A recommendation from the Centers for Disease Control and prevention and the American College of Sports Medicine}},
volume = {273},
year = {1995}
}