Journal
GENOME RESEARCH
Volume 13, Issue 4, Pages 579-588Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.668403
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Funding
- NEI NIH HHS [EY13010, R01 EY013010] Funding Source: Medline
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Cis-regulatory modules (CRMs) are transcription regulatory DNA segments (similar to1 Kb range) that control the expression of developmental genes in higher eukaryotes. We analyzed clustering of known binding motifs for transcription factors (TFs) in over 60 known CRMs from 20 Drosophila developmental genes, and we present evidence that each type of recognition motif forms significant clusters within the regulatory regions regulated by the corresponding TF. We demonstrate how a search with a single binding motif can be applied to explore gene regulatory networks and to discover coregulated genes in the genome. We also discuss the potential of the clustering method in interpreting the differential response of genes to various levels of transcriptional regulators.
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