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GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.

GeneSigDB (http://www.genesigdb.org or http://compbio.dfci.harvard.edu/genesigdb/) is a database of gene signatures that have been extracted and manually curated from the published literature. It provides a standardized resource of published prognostic, diagnostic and other gene signatures of cancer and related disease to the community so they can compare the predictive power of gene signatures or use these in gene set enrichment analysis. Since GeneSigDB release 1.0, we have expanded from 575 to 3515 gene signatures, which were collected and transcribed from 1604 published articles largely focused on gene expression in cancer, stem cells, immune cells, development and lung disease. We have made substantial upgrades to the GeneSigDB website to improve accessibility and usability, including adding a tag cloud browse function, facetted navigation and a 'basket' feature to store genes or gene signatures of interest. Users can analyze GeneSigDB gene signatures, or upload their own gene list, to identify gene signatures with significant gene overlap and results can be viewed on a dynamic editable heatmap that can be downloaded as a publication quality image. All data in GeneSigDB can be downloaded in numerous formats including .gmt file format for gene set enrichment analysis or as a R/Bioconductor data file. GeneSigDB is available from http://www.genesigdb.org.

Pubmed ID: 22110038


  • Culhane AC
  • Schröder MS
  • Sultana R
  • Picard SC
  • Martinelli EN
  • Kelly C
  • Haibe-Kains B
  • Kapushesky M
  • St Pierre AA
  • Flahive W
  • Picard KC
  • Gusenleitner D
  • Papenhausen G
  • O'Connor N
  • Correll M
  • Quackenbush J


Nucleic acids research

Publication Data

January 23, 2012

Associated Grants

  • Agency: NHGRI NIH HHS, Id: 1P50 HG004233
  • Agency: NLM NIH HHS, Id: 1R01 LM010129
  • Agency: NCI NIH HHS, Id: 1U19 CA148065
  • Agency: NHGRI NIH HHS, Id: P50 HG004233

Mesh Terms

  • Animals
  • Databases, Genetic
  • Gene Expression
  • Gene Expression Profiling
  • Humans
  • Mice
  • Rats
  • User-Computer Interface