TY - JOUR
T1 - GeneSetDB
T2 - A comprehensive meta-database, statistical and visualisation framework for gene set analysis
AU - Araki, Hiromitsu
AU - Knapp, Christoph
AU - Tsai, Peter
AU - Print, Cristin
N1 - Funding Information:
The authors gratefully acknowledge the developers of each source database for their permission to use their data in this study. The authors also thank Dr. Daniel Hurley and Ms. Vicky Fan for their useful comments and Dr. Enid Lam for her bioinformatic assistance with the development of a related database that contributed to GeneSetDB. H.A. is supported by FY 2010 Research Exchange Program between Royal Society of New Zealand and Japan Society for the Promotion of Science. Parts of this work have also been supported by NZ FoRST NERF contract 13296-NMTS-UOA, Maurice and Phyllis Paykel Trust contract 3624003, and a Maurice Wilkins Centre of Excellent grant.
PY - 2012
Y1 - 2012
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84861212058&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84861212058&partnerID=8YFLogxK
U2 - 10.1016/j.fob.2012.04.003
DO - 10.1016/j.fob.2012.04.003
M3 - Article
C2 - 23650583
AN - SCOPUS:84861212058
SN - 2211-5463
VL - 2
SP - 76
EP - 82
JO - FEBS Open Bio
JF - FEBS Open Bio
ER -
