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PMID: 15980575 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

WebGestalt: an integrated system for exploring gene sets in various biological contexts.

Nucleic acids research ·Vol. 33 ·No. Web Server issue ·2005-07-01 ·Pages W741-8

Zhang B, Kirov S, Snoddy J

Abstract

High-throughput technologies have led to the rapid generation of large-scale datasets about genes and gene products. These technologies have also shifted our research focus from 'single genes' to 'gene sets'. We have developed a web-based integrated data mining system, WebGestalt (http://genereg.ornl.gov/webgestalt/), to help biologists in exploring large sets of genes. WebGestalt is composed of four modules: gene set management, information retrieval, organization/visualization, and statistics. The management module uploads, saves, retrieves and deletes gene sets, as well as performs Boolean operations to generate the unions, intersections or differences between different gene sets. The information retrieval module currently retrieves information for up to 20 attributes for all genes in a gene set. The organization/visualization module organizes and visualizes gene sets in various biological contexts, including Gene Ontology, tissue expression pattern, chromosome distribution, metabolic and signaling pathways, protein domain information and publications. The statistics module recommends and performs statistical tests to suggest biological areas that are important to a gene set and warrant further investigation. In order to demonstrate the use of WebGestalt, we have generated 48 gene sets with genes over-represented in various human tissue types. Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php.

MeSH Terms
Computer Graphics Data Interpretation, Statistical Databases, Genetic Gene Expression Genes Genomics Humans Internet Proteomics Software Systems Integration Tissue Distribution User-Computer Interface
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Zhang Bing
Graduate School in Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
Kirov Stefan
Snoddy Jay
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gki475
Published
2005-07-01
Pages
W741-8
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1160236
Subset
IM
Grants
NIDA NIH HHS · P01 DA015027 · United States
NIAAA NIH HHS · R21 AA013532 · United States
NIDA NIH HHS · P01-DA015027 · United States
NIAAA NIH HHS · U01-AA013532 · United States
External Links
PubMed source DOI: 10.1093/nar/gki475 PMC Full Text View journal details
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