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Authors: Elena Stavrovskaya 1 ; Andrey Mironov 1 ; Dmitry Rodionov 2 ; Inna Dubchak 3 and Pavel Novichkov 3

Affiliations: 1 Moscow State University and Institute for Information Transmission Problems, Russian Federation ; 2 Institute for Information Transmission Problems and Burnham Institute for Medical Research, Russian Federation ; 3 Lawrence Berkeley National Laboratory, United States

Keyword(s): Regulation of transcription, Bacteria, Regulon, PWM.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering

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.

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Paper citation in several formats:
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 (BIOSTEC 2012) - BIOINFORMATICS; ISBN 978-989-8425-90-4; ISSN 2184-4305, SciTePress, pages 322-325. DOI: 10.5220/0003787403220325

@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 (BIOSTEC 2012) - BIOINFORMATICS},
year={2012},
pages={322-325},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003787403220325},
isbn={978-989-8425-90-4},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS
TI - AUTOMATED REGULON CONTENT PREDICTION AND ESTIMATION OF PWM QUALITY
SN - 978-989-8425-90-4
IS - 2184-4305
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
PB - SciTePress

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