AUTOMATED REGULON CONTENT PREDICTION AND ESTIMATION OF PWM QUALITY

Elena Stavrovskaya, Andrey Mironov, Dmitry Rodionov, Inna Dubchak, Pavel Novichkov

2012

Abstract

Identification of genes regulated by the same transcription factor (TF) is a major problem in analysis of regulation. The key step in detection of a group of co-regulated genes (regulon) is prediction of TF binding sites (TFBS). This is what positional weight matrix (PWM) is for. This matrix is applied to upstream region of a gene, and high-scoring sites are considered as putative TFBSs. Choice of threshold for the scoring function is a separate complicated problem. Usually, the threshold is chosen manually. Some methods for automated threshold detection exist, but they are based on selection of threshold for different functions. In this paper, we present an approach for regulon prediction based on a probabilistic method of threshold detection. The optimal probability computed by this method can be used to estimate the quality of the PWM itself. It can be useful when the matrix is a result of regulatory motif prediction program.

References

  1. Novichkov P. S., Laikova O. N., Novichkova E. S., Gelfand M. S., Arkin A. P., Dubchak I., Rodionov D. A., 2010. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. Jan;38(Database issue).
  2. Kalinina O. V., Mironov A. A., Gelfand M. S., Rakhmaninova A. B., 2004. Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci. Feb;13(2).
  3. Kotelnikova E. A, Makeev V. Yu, Gelfand M.S., 2005 Evolution of transcription factor DNA binding sites. Gene. 347 (2).
  4. Mironov A. A., Vinokurova N. P., Gel'falnd M. S., 2000. Software for analyzing bacterial genomes. Mol Biol (Mosk). 34(2).
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Paper Citation


in Harvard Style

Stavrovskaya E., Mironov A., Rodionov D., Dubchak I. and Novichkov P. (2012). AUTOMATED REGULON CONTENT PREDICTION AND ESTIMATION OF PWM QUALITY . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 322-325. DOI: 10.5220/0003787403220325


in Bibtex Style

@conference{bioinformatics12,
author={Elena Stavrovskaya and Andrey Mironov and Dmitry Rodionov and Inna Dubchak and Pavel Novichkov},
title={AUTOMATED REGULON CONTENT PREDICTION AND ESTIMATION OF PWM QUALITY},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={322-325},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003787403220325},
isbn={978-989-8425-90-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - AUTOMATED REGULON CONTENT PREDICTION AND ESTIMATION OF PWM QUALITY
SN - 978-989-8425-90-4
AU - Stavrovskaya E.
AU - Mironov A.
AU - Rodionov D.
AU - Dubchak I.
AU - Novichkov P.
PY - 2012
SP - 322
EP - 325
DO - 10.5220/0003787403220325