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Authors: Erola Pairo 1 ; Santiago Marco 1 and Alexandre Perera 2

Affiliations: 1 Universitat de Barcelona, Spain ; 2 CIBER de Bioingeniera, Materiales y Nanomedicina (CIBER-BBN), Spain

ISBN: 978-989-674-019-1

Keyword(s): Transcription factors, Binding sites, Numerical DNA, Principal components analysis, Missing values, BPCA.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Biostatistics and Stochastic Models ; Genomics and Proteomics ; Sequence Analysis

Abstract: Transcription Factor binding sites are short and degenerate sequences, located mostly at the promoter of the gene, where some proteins bind in order to regulate transcription. Locating these sequences is an important issue, and many experimental and computational methods have been developed. Algorithms to search binding sites are usually based on Position Specific Scoring Matrices (PSSM), where each position is treated independently. Mapping symbolical DNA to numerical sequences, a detector has been built with a Principal Component Analysis of the numerical sequences, taking into account covariances between positions. When a treatment of missing values is incorporated the Q-residuals detector, based on PCA, performs better than a PSSM algorithm. The performance on the detector depends on the estimation of missing values and the percentage of missing values considered in the model.

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Paper citation in several formats:
Pairo E.; Marco S.; Perera A. and (2010). A SUBSPACE METHOD FOR THE DETECTION OF TRANSCRIPTION FACTOR BINDING SITES.In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 102-107. DOI: 10.5220/0002697301020107

@conference{bioinformatics10,
author={Erola Pairo and Santiago Marco and Alexandre Perera},
title={A SUBSPACE METHOD FOR THE DETECTION OF TRANSCRIPTION FACTOR BINDING SITES},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={102-107},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002697301020107},
isbn={978-989-674-019-1},
}

TY - CONF

JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - A SUBSPACE METHOD FOR THE DETECTION OF TRANSCRIPTION FACTOR BINDING SITES
SN - 978-989-674-019-1
AU - Pairo, E.
AU - Marco, S.
AU - Perera, A.
PY - 2010
SP - 102
EP - 107
DO - 10.5220/0002697301020107

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