Some example sets of genes for motif search

This is a collection of sets of genes from Escherichia coli with know regulatory proteins binding to motifs in their upstream region. The data are taken from the motif database DPInteract. This allows to explore the applicability and limitations of the motif tools by comparing the results of motif searches with the experimentally verified motifs.

A regulon can be selected and the list of the corresponding genes submitted to the motif search tools. A list of motifs is given for comparison. These lists are compiled from entries in the DPInteract database. A link to the full description in the database is provided as well.

• Some regulons have strong motifs that are detected by all three motif search programs: lexA, tyrR, argR, purR.
• If there are only very few genes the Palindrome program succeeds in picking up motifs, if the motif is to some extend palindromic, where the other programs might fail: fadR, galR.
• If motifs are not palindromic only Gibbs or Alignace are able to detect them: hipB, phoB, torR.
• Gibbs seems to be slightly better in finding motifs in this simple setting: glpR, lrp

Notice that Gibbs and Alignace start from different seeds each time. If they do not find the correct motif the first time they might find it in a second or third trial. The use made of Gibbs, Alignace, or Palindrome in the tool page is very simplistic. More refined protocols for applying these programs are described in:

• Palindrome: M. S. Gelfand, E. V. Koonin, and A. A. Mironov, Prediction of transcription regulatory sites in Archaea by a comparative genomic approach, Nucl. Acid Res., 28(3):695-705, 2000, (Abstract).
• Alignace: J.D. Hughes, P.W. Estep, S. Tavazoie, G.M. Church, Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae, J. Mol. Biol., 296(5):1205-1214, 2000, (Abstract).