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LiteratureArticle Details
PMID: 16277751
Published · ppublish
English
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Validation Study
Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.
Abstract
Chromatin immunoprecipitation combined with microarray technology (Chip2) allows genome-wide determination of protein-DNA binding sites. The current standard method for analyzing Chip2 data requires additional control experiments that are subject to systematic error. We developed methods to assess significance using variance stabilization, learning error-model parameters without external control experiments. The method was validated experimentally, shows greater sensitivity than the current standard method, and incorporates false-discovery rate analysis. The corresponding software ('Chipper') is freely available. The method described here should help reveal an organism's transcription-regulatory 'wiring diagram'.
MeSH Terms
Analysis of Variance
Chromatin Immunoprecipitation
Computational Biology/methods
Models, Genetic
Oligonucleotide Array Sequence Analysis
Promoter Regions, Genetic
Software
Transcription Factors/metabolism
Chemicals
Transcription Factors
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
Published
2005-00-00
Epub
2005-00-01
Pages
R96
Language
English
Region
England
NLM ID
100960660
PMCID
PMC1297652
Subset
IM
Grants
NHGRI NIH HHS · U01 HG003147 · United States
NIGMS NIH HHS · GM30186 · United States
NIGMS NIH HHS · GM53720 · United States
NIGMS NIH HHS · R01 GM030186 · United States
NIGMS NIH HHS · R37 GM030186 · United States
NIGMS NIH HHS · R01 GM053720 · United States
NHGRI NIH HHS · HG003147 · United States
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