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Authors: Ramouna Fouladi 1 ; Emad Fatemizadeh 1 and S. Shahriar Arab 2

Affiliations: 1 Sharif University of Technology, Iran, Islamic Republic of ; 2 Faculty of Biological Sciences and Tarbiat Modares University, Iran, Islamic Republic of

ISBN: 978-989-8425-90-4

Keyword(s): Gene expression, Extended Kalman filtering, Gene regulatory network modelling.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Biostatistics and Stochastic Models ; Genomics and Proteomics ; Systems Biology

Abstract: In this paper, the Extended Kalman filtering (EKF) approach has been used to infer gene regulatory networks using time-series gene expression data. Gene expression values are considered stochastic processes and the gene regulatory network, a dynamical nonlinear stochastic model. Using these values and a modified Kalman filtering approach, the model’s parameters and consequently the interactions amongst genes are predicted. In this paper, each gene-gene interaction is modeled using a linear term, a nonlinear one, and a constant term. The linear and nonlinear term coefficients are included in the state vector together with the gene expressions’ true values. Through the extended Kalman filtering process, these coefficients are updated in such a way that the predicted gene expressions follow the ones observed. Finally, connections between each two genes are inferred based on these coefficients.

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Paper citation in several formats:
Fouladi, R.; Fatemizadeh, E.; Shahriar Arab, S. and Shahriar Arab, S. (2012). INFERENCE OF GENE REGULATORY NETWORKS BY EXTENDED KALMAN FILTERING USING GENE EXPRESSION TIME SERIES DATA.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 150-155. DOI: 10.5220/0003754801500155

@conference{bioinformatics12,
author={Ramouna Fouladi. and Emad Fatemizadeh. and S. Shahriar Arab. and S. Shahriar Arab.},
title={INFERENCE OF GENE REGULATORY NETWORKS BY EXTENDED KALMAN FILTERING USING GENE EXPRESSION TIME SERIES DATA},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={150-155},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003754801500155},
isbn={978-989-8425-90-4},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - INFERENCE OF GENE REGULATORY NETWORKS BY EXTENDED KALMAN FILTERING USING GENE EXPRESSION TIME SERIES DATA
SN - 978-989-8425-90-4
AU - Fouladi, R.
AU - Fatemizadeh, E.
AU - Shahriar Arab, S.
AU - Shahriar Arab, S.
PY - 2012
SP - 150
EP - 155
DO - 10.5220/0003754801500155

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