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

被引：56

作者：

Araki, Hiromitsu ^{[1
]}

Knapp, Christoph ^{[2
]}

Tsai, Peter ^{[2
]}

Print, Cristin ^{[1
,2
]}

机构：

[1] Univ Auckland, Fac Med & Hlth Sci, Sch Med Sci, Dept Mol Med & Pathol, Auckland 1, New Zealand

[2] Univ Auckland, Bioinformat Inst, Auckland 1, New Zealand

来源：

FEBS OPEN BIO | 2012年 / 2卷

基金：

日本学术振兴会;

关键词：

Database; Gene set; Enrichment analysis; Functional genomics; DNA METHYLATION; ENRICHMENT; SIGNATURES; RESOURCE; NETWORK; GENOME; ONTOLOGY; CELLS; TOOL;

D O I：

10.1016/j.fob.2012.04.003

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

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. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

引用

页码：76 / 82

页数：7

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