Identifying the promoter features governing differential kinetics of co-regulated genes using fuzzy expressions

Rocio Romero Zaliz, Oscar Harari, Cristina Rubio Escudero, Igor Zwir

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

One of the biggest challenges in genomics is the elucidation of the design principles controlling gene expression. Current approaches examine promoter sequences for particular features, such as the presence of binding sites for a transcriptional regulator, and identify recurrent relationships among these features termed network motifs. To define the expression dynamics of a group of genes, the strength of the connections in a network must be specified, and these are determined by the cis-promoter features participating in the regulation. Approaches that homogenize features among promoters (e.g., relying on consensuses to describe the various promoter features) and even across species hamper the discovery of the key differences that distinguish promoters that are co-regulated by the same transcriptional regulator. Thus, we have developed a an approach based on fuzzy logic expressions to analyze proteobacterial genomes for promoter features that is specifically designed to account for the variability in sequence, location and topology intrinsic to differential gene expression. We applied our method to characterize network motifs controlled by the PhoP/PhoQ regulatory system of Escherichia coli and Salmonella enterica serovar Typhimurium. We identify key features that enable the PhoP protein to produce distinct kinetic patterns in target genes, which could not have been uncovered just by inspecting network motifs.

Original languageEnglish
Title of host publication2007 IEEE International Conference on Fuzzy Systems, FUZZY
DOIs
StatePublished - 2007
Event2007 IEEE International Conference on Fuzzy Systems, FUZZY - London, United Kingdom
Duration: Jul 23 2007Jul 26 2007

Publication series

NameIEEE International Conference on Fuzzy Systems
ISSN (Print)1098-7584

Conference

Conference2007 IEEE International Conference on Fuzzy Systems, FUZZY
Country/TerritoryUnited Kingdom
CityLondon
Period07/23/0707/26/07

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