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Collections of fusion transcripts from various sources including those below. These data are leveraged by FusionAnnotator as integrated into the Trinity Cancer Transcriptome Analysis Toolkit Fusion-finding modules including STAR-Fusion and FusionInspector.
CTAT_HumanFusionLib currently integrates the following resources to help with identifying fusions known to be relevant to cancer biology as well as those that are more likely to be not relevant - known artifacts or fusions that tend to show up in normal samples.
| Label | Source Info |
|---|---|
| Mitelman | Known fusions from the Mitelman database |
| chimerdb_omim, chimerdb_pubmed | Fusions in OMIM and identified in Pubmed, as catalogued by ChimerDB2 |
| ChimerKB | represents a knowledgbase of fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences, derived from http://ercsb.ewha.ac.kr/fusiongene |
| ChimerPub | includes fusion genes obtained from text mining of PubMed abstracts, derived from http://ercsb.ewha.ac.kr/fusiongene |
| ChimerSeq | fusion candidates from TCGA as per FusionScan and TopHat-Fusion, derived from http://ercsb.ewha.ac.kr/fusiongene |
| Cosmic | Fusions listed in Cosmic |
| YOSHIHARA_TCGA | Fusion genes identified in cancer cell lines in The Cancer Genome Atlas based on previously published work by Yoshihara et al. |
| Klijn_CellLines | Fusions reported in Klijn et al. study of cancer cell lines http://www.ncbi.nlm.nih.gov/pubmed/25485619 |
| Larsson_TCGA | Recurrent fusions supported by genomic and transcriptomic data across cancer types, as per http://www.pnas.org/content/113/48/13768#T1 |
| CCLE | Fusions identified in cancer cell lines as part of the CCLE project |
| HaasMedCancer | Cancer-relevant fusions reported in the literature, as a supplement to other resources (ie. ChimerPub) and populated by yours truly (B. Haas) |
| FA_CancerSupp | Supplemental list of fusions predicted across thousands of various cancer samples (unpublished) |
| Label | Source Info |
|---|---|
| Oncogene | The oncogene label is applied to individual genes that are found in the list of oncogenes provided at http://www.bushmanlab.org/links/genelists |
| ArcherDX_panel | Gene is included in the Archer® FusionPlex® Solid Tumor Kit |
| FoundationOne_panel | Gene's included on Foundation Medicine's cancer gene listing. |
| OncocartaV1_panel | Genes on the OncoCarta v1 Panel |
| OncomapV4_panel | Genes on the OncoMap v4 Panel as described in PLoS One. 2012; 7(6): e38892. |
| Label | Source Info |
|---|---|
| GTEx | Fusions found recurrently in GTEx as mined using STAR-Fusion and FusionInspector (not published) |
| BodyMap | Fusions found by STAR-Fusion as applied to the Illumina Human Body Map reference data |
| DGD_PARALOGS | Duplicated genes as per the Duplicated Genes Database |
| HGNC_GENEFAM | HGNC gene family membership as per ftp://ftp.ebi.ac.uk/pub/databases/genenames/genefam_list.txt.gz |
| Greger_Normal | Fusion transcripts (mostly from tandem genes) detected based on analysis of RNA-Seq from 1000 genomes project samples. List derived from Greger et al. PLOS One, 2014 |
| Babiceanu_Normal | Recurrent chimeric fusion RNAs in non-cancer tissues and cells as per Babiceanu et al. NAR, 2016 |
| ConjoinG | Fused transcripts derived from the Conjoined Gene Database |
Other fusion-related resources, including most that overlap with the above are provided by Daniel Nicorici as part of FusionCatcher and described here.
** Contributions and pointers to additional resources to include are welcomed! **
Contact us at our Google forum: https://groups.google.com/forum/#!forum/trinity_ctat_users