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PMID: 23650583 Published · epublish English Journal Article

GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis.

FEBS open bio ·Vol. 2 ·2012-00-00 ·Pages 76-82

Araki H, Knapp C, Tsai P, Print C

Abstract

Most "omics" experiments require comprehensive interpretation of the biological meaning of gene lists. To address this requirement, a number of gene set analysis (GSA) tools have been developed. Although the biological value of GSA is strictly limited by the breadth of the gene sets used, very few methods exist for simultaneously analysing multiple publically available gene set databases. Therefore, we constructed GeneSetDB (http://genesetdb.auckland.ac.nz/haeremai.html), a comprehensive meta-database, which integrates 26 public databases containing diverse biological information with a particular focus on human disease and pharmacology. GeneSetDB enables users to search for gene sets containing a gene identifier or keyword, generate their own gene sets, or statistically test for enrichment of an uploaded gene list across all gene sets, and visualise gene set enrichment and overlap using a clustered heat map.

Keywords
Database Enrichment analysis Functional genomics GSA gene set analysis Gene set
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Araki Hiromitsu
Department of Molecular Medicine & Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
Knapp Christoph
Tsai Peter
Print Cristin
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Article Info
Journal
FEBS open bio
Abbr.
FEBS Open Bio
ISSN
2211-5463
DOI
10.1016/j.fob.2012.04.003
Published
2012-00-00
Epub
2012-00-17
Pages
76-82
Language
English
Region
England
NLM ID
101580716
PMCID
PMC3642118
External Links
PubMed source DOI: 10.1016/j.fob.2012.04.003 PMC Full Text View journal details
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