BioXpress ReadTheDocs Notes

[seankim658]

Source: https://bioxpress.readthedocs.io/en/latest/index.html#

• Step 1 Downloader link https://portal.gdc.cancer.gov/repository is dead

[mariacuria]

Here is the location of BioXpress processed files in the GlyGen server

Folder - /data/projects/glygen/downloads/bioxpress/2021_08/

Disease Expression - /data/projects/glygen/downloads/bioxpress/2021_08/bioxpress_disease.csv

Example row:

colname	value
gene_symbol	GABRB2
uniprotkb_ac	P47870
refseq_ac	NP_068711.1
log2fc	7.14
pvalue	1.11E-201
adjpvalue	4.20E-197
significance	Yes
direction	up
data_source	TCGA
cancer_type	thyroid cancer
doid	1781
do_name	DOID:1781 / thyroid cancer
parent_doid	1781
parent_name	DOID:1781 / thyroid cancer
uberon_id	2046
pmid	-
sample_name	DOID:1781 / thyroid cancer
sample_id	16
total_samples_tumor	502
total_samples_normal	58

Normal Expression - /data/projects/glygen/downloads/bioxpress/2021_08/bioxpress_normal.csv

Example row:

colname	value
uniprotkb_ac	A0A075B6F4
ensembl_gene_id	ENSG00000183938
uberon_anatomical_id	UBERON:0002367
uberon_anatomical_name	prostate gland
uberon_developmental_id	HsapDv:0000087
uberon_developmental_name	human adult stage (human)
expression_level_gene_relative	LOW
expression_level_anatomical_relative	LOW
call_quality	SILVER
expression_rank_score	4.20E+04
expression_score	23.69