GeneSigDB--a curated database of gene expression signatures.

Nucleic Acids Research
Aedín C CulhaneJohn Quackenbush

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, a...Continue Reading

References

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Citations

Jun 22, 2011·Human Genetics·Kristen Fortney, Igor Jurisica
May 7, 2011·Bioinformatics·Arthur LiberzonJill P Mesirov
Jul 14, 2012·Bioinformatics·Daniel GusenleitnerAedín C Culhane
Jun 12, 2013·Bioinformatics·Christopher M TanAvi Ma'ayan
Oct 1, 2011·Database : the Journal of Biological Databases and Curation·Khader ShameerRamanathan Sowdhamini
Jan 21, 2012·Journal of the National Cancer Institute·Benjamin Haibe-KainsChristos Sotiriou
May 25, 2010·Nucleic Acids Research·Jignesh R ParikhNils Blüthgen
Jan 21, 2012·Nucleic Acids Research·George C TsengEleanor Feingold
Nov 24, 2011·Nucleic Acids Research·Aedín C CulhaneJohn Quackenbush
Nov 9, 2012·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Levi WaldronCurtis Huttenhower
Nov 15, 2011·BMC Bioinformatics·Jeffrey T ChangJoseph R Nevins
Jul 4, 2012·BMC Bioinformatics·Ruth DannenfelserAvi Ma'ayan
Apr 17, 2013·BMC Bioinformatics·Edward Y ChenAvi Ma'ayan
Jul 20, 2012·BMC Systems Biology·Jianxin WangYi Pan
Dec 18, 2013·PloS One·Sarah C PreissnerSaskia Preissner
Mar 23, 2011·Bioinformatics and Biology Insights·Markus SchmidbergerUlrich Mansmann
Aug 3, 2013·Briefings in Bioinformatics·Irene KouskoumvekakiSøren Brunak
Jun 16, 2011·Journal of the American Medical Informatics Association : JAMIA·James L ChenYves A Lussier
Apr 14, 2012·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·Yan KouAvi Ma'ayan
Jun 10, 2014·Journal of Theoretical Biology·Xiaogang WuJake Yue Chen
Jan 30, 2015·Genome Biology·Olivier GevaertSylvia K Plevritis
Nov 21, 2015·PLoS Computational Biology·Kimberly Glass, Michelle Girvan
Jul 5, 2016·Expert Review of Neurotherapeutics·Francesco PanzaDavide Seripa
Jul 5, 2016·Database : the Journal of Biological Databases and Curation·Andrew D RouillardAvi Ma'ayan
Jan 28, 2017·Current Opinion in Genetics & Development·Jasper WoutersStein Aerts
Jan 26, 2017·BioTechniques·Mahjoubeh Jalali Sefid Dashti, Junaid Gamieldien

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Software Mentioned

Apache Lucene
EnsEMBL
SigID
maptrace
jQuery
Unigene
GeneSigDB
Excel
MSigDB
Apache Tomcat

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