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PMID: 16423281 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.

BMC bioinformatics ·Vol. 7 ·2006-01-19 ·Pages 30

Yi M, Horton JD, Cohen JC, Hobbs HH, Stephens RM

Abstract

Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-genomic era is to assemble the large amounts of data generated into a meaningful biological context. We have developed a comprehensive software tool, WholePathwayScope (WPS), for deriving biological insights from analysis of HTP data. WPS extracts gene lists with shared biological themes through color cue templates. WPS statistically evaluates global functional category enrichment of gene lists and pathway-level pattern enrichment of data. WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or groups, and explores gene-term relationships within the derived gene-term association networks (GTANs). WPS simultaneously compares multiple datasets within biological contexts either as pathways or as association networks. WPS also integrates Genetic Association Database and Partial MedGene Database for disease-association information. We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. Application examples demonstrated the capacity of WPS to significantly facilitate the analysis of HTP data for integrative discovery. This tool represents a pathway-based platform for discovery integration to maximize analysis power. The tool is freely available at http://www.abcc.ncifcrf.gov/wps/wps_index.php.

MeSH Terms
Computer Graphics Database Management Systems Databases, Genetic Gene Expression Profiling/methods Gene Expression Regulation/physiology Information Storage and Retrieval/methods Models, Biological Oligonucleotide Array Sequence Analysis/methods Signal Transduction/physiology Software User-Computer Interface
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Yi Ming
Advanced Biomedical Computing Center, National Cancer Institute-Frederick/SAIC-Frederick Inc., Frederick, MD 21702, USA. myi@ncifcrf.gov
Horton Jay D
Cohen Jonathan C
Hobbs Helen H
Stephens Robert M
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Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-7-30
Email
myi@ncifcrf.gov
Published
2006-01-19
Epub
2006-00-19
Pages
30
Language
English
Region
England
NLM ID
100965194
PMCID
PMC1388242
Subset
IM
Grants
NHLBI NIH HHS · UO1 HL66880 · United States
NHLBI NIH HHS · R01 HL072304 · United States
NCI NIH HHS · N01CO12400 · United States
NHLBI NIH HHS · U01 HL066880 · United States
NCI NIH HHS · N01-CO-12400 · United States
NHLBI NIH HHS · R01 HL72304 · United States
External Links
PubMed source DOI: 10.1186/1471-2105-7-30 PMC Full Text View journal details
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