Gene Promoter Scan Methodology for Identifying and Classifying Coregulated Promoters

Igor Zwir, Oscar Harari, Eduardo A. Groisman

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Scopus citations


A critical challenge of the postgenomic era is to understand how genes are differentially regulated. Genetic and genomic approaches have been used successfully to assign genes to distinct regulatory networks in both prokaryotes and eukaryotes. However, little is known about what determines the differential expression of genes within a particular network, even when it involves a single transcription factor. The fact that coregulated genes may be differentially expressed suggests that subtle differences in the shared cis-acting regulatory elements are likely to be significant. This chapter describes a method, termed gene promoter scan (GPS), that discriminates among coregulated promoters by simultaneously considering a variety of cis-acting regulatory features. Application of this method to the PhoP/PhoQ two-component regulatory system of Escherichia coli and Salmonella enterica uncovered novel members of the PhoP regulon, as well as regulatory interactions that had not been discovered using previous approaches. The predictions made by GPS were validated experimentally to establish that the PhoP protein uses multiple mechanisms to control gene transcription and is a central element in a highly connected network.

Original languageEnglish
Title of host publicationTwo Component Signaling Systems, Part A
PublisherAcademic Press Inc.
Number of pages25
StatePublished - Jan 1 2007
Externally publishedYes

Publication series

NameMethods in Enzymology
ISSN (Print)0076-6879

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    Zwir, I., Harari, O., & Groisman, E. A. (2007). Gene Promoter Scan Methodology for Identifying and Classifying Coregulated Promoters. In Two Component Signaling Systems, Part A (pp. 361-385). (Methods in Enzymology; Vol. 422). Academic Press Inc..