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Nucleic Acids Research Advance Access originally published online on November 25, 2008
Nucleic Acids Research 2009 37(1):1-13; doi:10.1093/nar/gkn923
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Nucleic Acids Research, 2009, Vol. 37, No. 1 1-13
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Survey and Summary

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

Da Wei Huang, Brad T. Sherman and Richard A. Lempicki*

Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, MD 21702, USA

*To whom correspondence should be addressed. Tel: +1 301 846 5093; Fax: +1 301 846 6762; Email: rlempicki{at}mail.nih.gov

Received September 10, 2008. Revised October 24, 2008. Accepted November 3, 2008.

Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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