Transcription factor binding element detection using functional clustering of mutant expression data

Chen, G., Hata, N., Zhang, M. Q. (2004) Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Res, 32 (8). pp. 2362-71. ISSN 1362-4962 (Electronic)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/15115798
DOI: 10.1093/nar/gkh557

Abstract

As a powerful tool to reveal gene functions, gene mutation has been used extensively in molecular biology studies. With high throughput technologies, such as DNA microarray, genome-wide gene expression changes can be monitored in mutants. Here we present a simple approach to detect the transcription-factor-binding motif using microarray expression data from a mutant in which the relevant transcription factor is deleted. A core part of our approach is clustering of differentially expressed genes based on functional annotations, such as Gene Ontology (GO). We tested our method with eight microarray data sets from the Rosetta Compendium and were able to detect canonical binding motifs for at least four transcription factors. With the support of chromatin IP chip data, we also predict a possible variant of the Swi4 binding motif and recover a core motif for Arg80. Our approach should be readily applicable to microarray experiments using other types of molecular biology techniques, such as conditional knockout/overexpression or RNAi-mediated 'knockdown', to perturb the expression of a transcription factor. Functional clustering included in our approach may also provide new insights into the function of the relevant transcription factor.

Item Type: Paper
Uncontrolled Keywords: Base Sequence Cluster Analysis Computational Biology/ methods Consensus Sequence/genetics Gene Deletion Gene Expression Profiling Genes, Fungal/genetics Genomics/ methods Oligonucleotide Array Sequence Analysis Reproducibility of Results Response Elements/ genetics Saccharomyces cerevisiae Proteins/genetics/metabolism Software Transcription Factors/ genetics/ metabolism
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > Mapping and Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification
bioinformatics > genomics and proteomics > Mapping and Rendering > ontology
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: 2004
Date Deposited: 04 Mar 2013 21:35
Last Modified: 08 Nov 2017 15:51
PMCID: PMC419446
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27702

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