Journal Article

Statistical detection of cooperative transcription factors with similarity adjustment

Utz J. Pape, Holger Klein and Martin Vingron

in Bioinformatics

Volume 25, issue 16, pages 2103-2109
Published in print August 2009 | ISSN: 1367-4803
Published online March 2009 | e-ISSN: 1460-2059 | DOI:

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Motivation: Statistical assessment of cis-regulatory modules (CRMs) is a crucial task in computational biology. Usually, one concludes from exceptional co-occurrences of DNA motifs that the corresponding transcription factors (TFs) are cooperative. However, similar DNA motifs tend to co-occur in random sequences due to high probability of overlapping occurrences. Therefore, it is important to consider similarity of DNA motifs in the statistical assessment.

Results: Based on previous work, we propose to adjust the window size for co-occurrence detection. Using the derived approximation, one obtains different window sizes for different sets of DNA motifs depending on their similarities. This ensures that the probability of co-occurrences in random sequences are equal. Applying the approach to selected similar and dissimilar DNA motifs from human TFs shows the necessity of adjustment and confirms the accuracy of the approximation by comparison to simulated data. Furthermore, it becomes clear that approaches ignoring similarities strongly underestimate P-values for cooperativity of TFs with similar DNA motifs. In addition, the approach is extended to deal with overlapping windows. We derive Chen–Stein error bounds for the approximation. Comparing the error bounds for similar and dissimilar DNA motifs shows that the approximation for similar DNA motifs yields large bounds. Hence, one has to be careful using overlapping windows. Based on the error bounds, one can precompute the approximation errors and select an appropriate overlap scheme before running the analysis.

Availability: Software to perform the calculation for pairs of position frequency matrices (PFMs) is available at as well as C++ source code for downloading.


Journal Article.  5680 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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