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TissGDB: tissue-specific gene database in cancer.

Pora Kim1, Aekyung Park1,2, Guangchun Han1

  • 1Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

Nucleic Acids Research
|October 17, 2017
PubMed
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We developed TissGDB, a database of 2461 tissue-specific genes (TissGenes) across 22 tissues. This resource aids in understanding cancer mechanisms and discovering therapeutic targets by analyzing gene expression and mutations in 28 cancer types.

Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Tissue-specific gene expression is crucial for understanding biological processes and diseases.
  • Identifying tissue-specific genes (TissGenes) offers insights into disease mechanisms and organ-specific therapeutic targets.

Purpose of the Study:

  • To build TissGDB (Tissue specific Gene DataBase in cancer), a comprehensive resource for tissue-specific genes in cancer.
  • To analyze tissue-specific gene features across 28 cancer types using The Cancer Genome Atlas (TCGA) data.

Main Methods:

  • Collected and curated 2461 TissGenes from The Human Protein Atlas (HPA), TiGER, and GTEx across 22 tissue types.
  • Performed gene expression, somatic mutation, and prognostic marker analyses on TissGenes using TCGA data for 28 cancer types.

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Main Results:

  • Identified hundreds of TissGenes with conserved or altered tissue-specific expression across cancer types.
  • Discovered TissGenes with cancer type-specific isoform expression, fusions with oncogenes/tumor suppressors, and prognostic significance.

Conclusions:

  • TissGDB provides valuable annotations including gene expression, mutations, and clinical relevance for TissGenes.
  • The TissGDB database facilitates the discovery of clinically relevant genes and mutations for cancer research and therapeutic development.