Volume 84, Number 1, October 2008
Article Number 18001
Number of page(s) 6
Section Interdisciplinary Physics and Related Areas of Science and Technology
Published online 15 September 2008
EPL, 84 (2008) 18001
DOI: 10.1209/0295-5075/84/18001

Identifying short motifs by means of extreme value analysis

D. Bianchi and B. Tirozzi

Dipartimento di Fisica, Università di Roma “La Sapienza” - p.le Aldo Moro 2, 00185 Rome, Italy, EU

received 1 April 2008; accepted in final form 13 August 2008; published October 2008
published online 15 September 2008

The problem of detecting a binding site —a substring of DNA where transcription factors attach— on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability can display large fluctuations from one putative binding site to another. Here we use a self-consistent statistical procedure that accounts correctly for the large deviations of the matching probability to predict the location of short binding sites. We apply it in two distinct situations: a) the detection of the binding sites for three specific transcription factors on a set of 134 estrogen-regulated genes; b) the identification, in a set of 138 possible transcription factors, of the ones binding a specific set of nine genes. In both instances, experimental findings are reproduced (when available) and the number of false positives is significantly reduced with respect to the other methods commonly employed.

87.10.Vg - Biological information.
02.50.Tt - Inference methods.
87.18.Vf - Systems biology.

© EPLA 2008