Nucleotide variation of regulatory motifs may lead to distinct expression patterns

Nucleotide variation of regulatory motifs may lead to distinct expression patterns Bioinformatics 23 (13), i440-i449

Year

2007

Category

Bioonformatics

Journal

Bioinformatics

Type

General

Authors

L Segal, M Lapidot, Z Solan, E Ruppin, Y Pilpel, D Horn

Abstract

Motivation: Current methodologies for the selection of putative transcription factor binding sites (TFBS) rely on various assumptions such as over-representation of motifs occurring on gene promoters, and the use of motif descriptions such as consensus or position-specific scoring matrices (PSSMs). In order to avoid bias introduced by such assumptions, we apply an unsupervised motif extraction (MEX) algorithm to sequences of promoters. The extracted motifs are assessed for their likely cis-regulatory function by calculating the expression coherence (EC) of the corresponding genes, across a set of biological conditions.

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