Open Access

Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model

  • Jia Meng1,
  • Jianqiu(Michelle) Zhang1,
  • Yuan(Alan) Qi2,
  • Yidong Chen3, 4 and
  • Yufei Huang1, 3, 4Email author
EURASIP Journal on Advances in Signal Processing20102010:538919

https://doi.org/10.1155/2010/538919

Received: 2 April 2010

Accepted: 11 June 2010

Published: 13 July 2010

Abstract

The problem of uncovering transcriptional regulation by transcription factors (TFs) based on microarray data is considered. A novel Bayesian sparse correlated rectified factor model (BSCRFM) is proposed that models the unknown TF protein level activity, the correlated regulations between TFs, and the sparse nature of TF-regulated genes. The model admits prior knowledge from existing database regarding TF-regulated target genes based on a sparse prior and through a developed Gibbs sampling algorithm, a context-specific transcriptional regulatory network specific to the experimental condition of the microarray data can be obtained. The proposed model and the Gibbs sampling algorithm were evaluated on the simulated systems, and results demonstrated the validity and effectiveness of the proposed approach. The proposed model was then applied to the breast cancer microarray data of patients with Estrogen Receptor positive ( ) status and Estrogen Receptor negative ( ) status, respectively.

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Authors’ Affiliations

(1)
Department of Electrical and Computer Engineering, University of Texas at San Antonio
(2)
Departments of Computer Science and Statistics, Purdue University
(3)
Department of Epidemiology and Biostatistics, UT Health Science Center at San Antonio
(4)
Greehey Children's Cancer Research Institute, UT Health Science Center at San Antonio

Copyright

© Jia Meng et al. 2010

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.