Application of gene set enrichment method to ChIP-chip data analysis

Yidong Chen, Fan Yang, Paul S. Meltzer

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

To elucidate biological functions from gene expression profiles, gene set enrichment analysis (GSEA) is widely applied against sets of predefined genes that may yield crucial clues to their functional themes or regulatory information. However, gene list derived from array-based chromatin- immunoprecipitation (ChIP-chip) experiments, where all genes with one or more binding sites of a given protein, possesses different characteristics than that from gene expression profiles: genes are not rank-ordered by their differential expression, but rather associated with a genomic distance to its nearest binding site from the transcription start site (TSS). In this study, we proposed a unique binding-site enrichment analysis method that enabled enrichment analysis of gene list derived from whole-genome ChIP-chip experiment to gene expression data set, such as a panel of normal tissue gene expression profiles or some cancer-related expression profiles, in order to identify the essential regulatory role of the transcription factor under study.

Original languageEnglish (US)
Title of host publicationGENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics
DOIs
StatePublished - Sep 17 2008
Externally publishedYes
Event6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08 - Phoenix, AZ, United States
Duration: Jun 8 2008Jun 10 2008

Publication series

NameGENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics

Other

Other6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08
CountryUnited States
CityPhoenix, AZ
Period6/8/086/10/08

ASJC Scopus subject areas

  • Genetics
  • Signal Processing
  • Electrical and Electronic Engineering
  • Statistics, Probability and Uncertainty

Fingerprint Dive into the research topics of 'Application of gene set enrichment method to ChIP-chip data analysis'. Together they form a unique fingerprint.

  • Cite this

    Chen, Y., Yang, F., & Meltzer, P. S. (2008). Application of gene set enrichment method to ChIP-chip data analysis. In GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics [4555684] (GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics). https://doi.org/10.1109/GENSIPS.2008.4555684