TissGDB: tissue-specific gene database in cancer.

Abstract:

:Tissue-specific gene expression is critical in understanding biological processes, physiological conditions, and disease. The identification and appropriate use of tissue-specific genes (TissGenes) will provide important insights into disease mechanisms and organ-specific therapeutic targets. To better understand the tissue-specific features for each cancer type and to advance the discovery of clinically relevant genes or mutations, we built TissGDB (Tissue specific Gene DataBase in cancer) available at http://zhaobioinfo.org/TissGDB. We collected and curated 2461 tissue specific genes (TissGenes) across 22 tissue types that matched the 28 cancer types of The Cancer Genome Atlas (TCGA) from three representative tissue-specific gene expression resources: The Human Protein Atlas (HPA), Tissue-specific Gene Expression and Regulation (TiGER), and Genotype-Tissue Expression (GTEx). For these 2461 TissGenes, we performed gene expression, somatic mutation, and prognostic marker-based analyses across 28 cancer types using TCGA data. Our analyses identified hundreds of TissGenes, including genes that universally kept or lost tissue-specific gene expression, with other features: cancer type-specific isoform expression, fusion with oncogenes or tumor suppressor genes, and markers for protective or risk prognosis. TissGDB provides seven categories of annotations: TissGeneSummary, TissGeneExp, TissGene-miRNA, TissGeneMut, TissGeneNet, TissGeneProg, TissGeneClin.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Kim P,Park A,Han G,Sun H,Jia P,Zhao Z

doi

10.1093/nar/gkx850

subject

Has Abstract

pub_date

2018-01-04 00:00:00

pages

D1031-D1038

issue

D1

eissn

0305-1048

issn

1362-4962

pii

4210940

journal_volume

46

pub_type

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