Computational discovery of gene modules and regulatory networks
- 12 October 2003
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Biotechnology
- Vol. 21 (11), 1337-1342
- https://doi.org/10.1038/nbt890
Abstract
We describe an algorithm for discovering regulatory networks of gene modules, GRAM (Genetic Regulatory Modules), that combines information from genome-wide location and expression data sets. A gene module is defined as a set of coexpressed genes to which the same set of transcription factors binds. Unlike previous approaches1,2,3,4,5 that relied primarily on functional information from expression data, the GRAM algorithm explicitly links genes to the factors that regulate them by incorporating DNA binding data, which provide direct physical evidence of regulatory interactions. We use the GRAM algorithm to describe a genome-wide regulatory network in Saccharomyces cerevisiae using binding information for 106 transcription factors profiled in rich medium conditions data* from over 500 expression experiments. We also present a genome-wide location analysis data set for regulators in yeast cells treated with rapamycin, and use the GRAM algorithm to provide biological insights into this regulatory network. *Note: In the version of this article initially published online, the word "and" was omitted from the fourth sentence of the abstract, altering the meaning. The sentence should read: "We use the GRAM algorithm to describe a genome-wide regulatory network in Saccharomyces cerevisiae using binding information for 106 transcription factors profiled in rich medium conditions and data from over 500 expression experiments." This mistake has been corrected for the HTML and print versions of the article.Keywords
This publication has 32 references indexed in Scilit:
- Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataNature Genetics, 2003
- TRANSFAC(R): transcriptional regulation, from patterns to profilesNucleic Acids Research, 2003
- Transcriptional Regulatory Networks in Saccharomyces cerevisiaeScience, 2002
- Revealing modular organization in the yeast transcriptional networkNature Genetics, 2002
- Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genomeProceedings of the National Academy of Sciences of the United States of America, 2002
- MIPS: a database for genomes and protein sequencesNucleic Acids Research, 2002
- Identifying regulatory networks by combinatorial analysis of promoter elementsNature Genetics, 2001
- Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer.Genes & Development, 1989
- The GCR1 gene encodes a positive transcriptional regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families in Saccharomyces cerevisiae.Molecular and Cellular Biology, 1987
- Glycolytic gene expression in Saccharomyces cerevisiae: nucleotide sequence of GCR1, null mutants, and evidence for expression.Molecular and Cellular Biology, 1986