title: GeneSigDB--a curated database of gene expression signatures.
abstract: The primary objective of most gene expression studies is the identification of one or more gene signatures; lists of genes whose transcriptional levels are uniquely associated with a specific biological phenotype. Whilst thousands of experimentally derived gene signatures are published, their potential value to the community is limited by their computational inaccessibility. Gene signatures are embedded in published article figures, tables or in supplementary materials, and are frequently presented using non-standard gene or probeset nomenclature. We present GeneSigDB (http://compbio.dfci.harvard.edu/genesigdb) a manually curated database of gene expression signatures. GeneSigDB release 1.0 focuses on cancer and stem cells gene signatures and was constructed from more than 850 publications from which we manually transcribed 575 gene signatures. Most gene signatures (n = 560) were successfully mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. The GeneSigDB web portal is easy to search, allows users to compare their own gene list to those in the database, and download gene signatures in most common gene identifier formats.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA. johnq@jimmy.harvard.edu
authors.forename: Aedín C
authors.initials: AC
authors.lastname: Culhane
authors.forename: Thomas
authors.initials: T
authors.lastname: Schwarzl
authors.forename: Razvan
authors.initials: R
authors.lastname: Sultana
authors.forename: Kermshlise C
authors.initials: KC
authors.lastname: Picard
authors.forename: Shaita C
authors.initials: SC
authors.lastname: Picard
authors.forename: Tim H
authors.initials: TH
authors.lastname: Lu
authors.forename: Katherine R
authors.initials: KR
authors.lastname: Franklin
authors.forename: Simon J
authors.initials: SJ
authors.lastname: French
authors.forename: Gerald
authors.initials: G
authors.lastname: Papenhausen
authors.forename: Mick
authors.initials: M
authors.lastname: Correll
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D009369:Neoplasms / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D013234:Stem Cells / Q000166:cytology*