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Garnet - gene set analysis with exploration of annotation relations

Title
Garnet - gene set analysis with exploration of annotation relations
Authors
Rho K.Kim B.Jang Y.Lee S.Bae T.Seo J.Seo C.Lee J.Kang H.Yu U.Kim S.Kim W.K.
Ewha Authors
이상혁김완규
SCOPUS Author ID
이상혁scopus; 김완규scopus
Issue Date
2011
Journal Title
BMC Bioinformatics
ISSN
1471-2105JCR Link
Citation
BMC Bioinformatics vol. 12, no. SUPPL. 1
Indexed
SCIE; SCOPUS WOS scopus
Document Type
Article
Abstract
Background: Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO) terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information.Results: GARNET (Gene Annotation Relationship NEtwork Tools) is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules - gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations.Conclusions: GARNET (gene annotation relationship network tools) is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (http://garnet.isysbio.org/ or http://ercsb.ewha.ac.kr/garnet/). © 2011 Rho1 et al; licensee BioMed Central Ltd.
DOI
10.1186/1471-2105-12-S1-S25
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자연과학대학 > 생명과학전공 > Journal papers
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