title: GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.
abstract: 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.
authors: Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. aedin@jimmy.harvard.edu
authors: Aedín C
authors: AC
authors: Culhane
authors: Markus S
authors: MS
authors: Schröder
authors: Razvan
authors: R
authors: Sultana
authors: Shaita C
authors: SC
authors: Picard
authors: Enzo N
authors: EN
authors: Martinelli
authors: Caroline
authors: C
authors: Kelly
authors: Benjamin
authors: B
authors: Haibe-Kains
authors: Misha
authors: M
authors: Kapushesky
authors: Anne-Alyssa
authors: AA
authors: St Pierre
authors: William
authors: W
authors: Flahive
authors: Kermshlise C
authors: KC
authors: Picard
authors: Daniel
authors: D
authors: Gusenleitner
authors: Gerald
authors: G
authors: Papenhausen
authors: Niall
authors: N
authors: O'Connor
authors: Mick
authors: M
authors: Correll
authors: John
authors: J
authors: Quackenbush
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D051381:Rats; D014584:User-Computer Interface