Identifying biologically significant pathways by gene set enrichment analysis using fisher's criterion

Jaeyoung Kim, Hyungmin Lee, Miyoung Shin

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Gene set enrichment analysis (GSEA) is a computational method to identify statistically significant genesets showing differential expression between two groups. In particular, unlike other previous approaches, this enables us to uncover their biological meanings in an elegant way by providing a unified analytical framework that employs a priori known biological knowledges along with gene expression profiles during the analysis procedure. For original GSEA, all the genes in a given dataset are ordered by the signal-to-noise ratio of their microarray expression profiles between two groups and then further analyses are proceeded. Despite of its impressive results in previous studies with original GSEA, however, gene ranking by the signal-to-noise ratio makes it difficult to extract both highly up-regulated genes and highly down-regulated genes at a time as significant genes, which may not reflect such situations as incurred in metabolic and signaling pathways. Thus, it is necessary to make further investigation for better finding of biologically significant pathways. To deal with this problem, in this article, we explore the method of gene set enrichment analysis with Fisher's criterion for gene ranking, named FC-GSEA, and evaluate its effects made in Leukemia related pathway analyses.

Original languageEnglish
Title of host publicationProceedings of the 2008 2nd International Conference on Future Generation Communication and Networking, FGCN 2008 and BSBT 2008
Subtitle of host publication2008 International Conference on Bio-Science and Bio-Technology
Pages63-66
Number of pages4
DOIs
StatePublished - 2008
Event2008 International Conference on Bio-Science and Bio-Technology, BSBT 2008, held in conjunction with 2008 2nd International Conference on Future Generation Communication and Networking, FGCN 2008 - Hainan Island, China
Duration: 13 Dec 200815 Dec 2008

Publication series

NameProceedings of the 2008 2nd International Conference on Future Generation Communication and Networking, FGCN 2008 and BSBT 2008: 2008 International Conference on Bio-Science and Bio-Technology
Volume3

Conference

Conference2008 International Conference on Bio-Science and Bio-Technology, BSBT 2008, held in conjunction with 2008 2nd International Conference on Future Generation Communication and Networking, FGCN 2008
Country/TerritoryChina
CityHainan Island
Period13/12/0815/12/08

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