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About the Authors:
Bin Yan
* E-mail: [email protected](MZ); [email protected] (ZC); [email protected] (BY)
Affiliation: Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
Huai Li
Affiliation: Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
Xinping Yang
Affiliation: Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorder, National Institutes of Health, Bethesda, Maryland, United States of America
Jiaofang Shao
Affiliation: Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
Minyoung Jang
Affiliations Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorder, National Institutes of Health, Bethesda, Maryland, United States of America, Clinical Research Training Program, sponsored by National Institutes of Health and Pfizer, Bethesda, Maryland, United States of America
Daogang Guan
Affiliation: Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
Sige Zou
Affiliation: Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
Carter Van Waes
Affiliation: Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorder, National Institutes of Health, Bethesda, Maryland, United States of America
Zhong Chen
* E-mail: [email protected](MZ); [email protected] (ZC); [email protected] (BY)
Affiliation: Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorder, National Institutes of Health, Bethesda, Maryland, United States of America
Ming Zhan
* E-mail: [email protected](MZ); [email protected] (ZC); [email protected] (BY)
Affiliation: Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, Texas, United States of America
Introduction
Transcriptional regulation of genes is governed by a combinatorial operation of multiple transcription factors (TFs) and microRNAs (miRNAs) at transcriptional and post-transcriptional levels. These factors can organize regulatory modules and thereby control expression of a set of genes in networks that carry out a variety of functional processes. Therefore, identification of regulatory modules and gene networks is critical for understanding molecular mechanisms of transcriptional regulation in complex biological systems. Various mathematical algorithms or computational methods have been developed for integrative analysis of microarray gene expression and TF binding data to predict target genes of TFs, such as Bayesian hierarchical network [1], Bayesian multivariate modeling [2], matrix decomposition [3] and regression model [4]. Based on predicted target genes of multiple TFs, we can unravel transcriptional regulatory modules and reconstruct gene networks. Among these methods, matrix decomposition...