Title: Inference of hierarchical regulatory network of TCF7L2 binding sites in MCF7 cell line

Authors: Yao Wang; Rui Wang; Victor X. Jin

Addresses: Departments of Molecular Medicine and Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA ' School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China ' Departments of Molecular Medicine and Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA

Abstract: The TCF7L2 transcription factor (TF) is a member of Wnt signalling pathway, and may influence transcription of several genes by binding to distinct regulatory regions. Genome-wide studies have identified thousands of TCF7L2 binding sites and have revealed some associated TF partners. However, there is still a large uncharted region in the hierarchical regulatory network for TCF7L2 and the partner TFs in MCF7 cells. We analysed ChIP-seq data by searching for motifs in the enriched peak region based on TF-specific position weight matrix (PWM). We found association of FOXO1 and CAD with up-regulated genes, AP2α, PBF and AP1 with down-regulated genes. TCF7L2 and GATA3 were found to be associated with both up and down-regulated genes. Our study uncovers new TCF7L2 associated regulatory networks by mining ChIP-seq data in MCF7 cell, which may contribute to further study of the mechanisms related to Wnt pathway in breast cancer or other diseases.

Keywords: motifs; hierarchical regulatory networks; TCF7L2 transcription factor; TCF7L2 binding sites; MCF7 cell lines; data mining; breast cancer.

DOI: 10.1504/IJCBDD.2016.074990

International Journal of Computational Biology and Drug Design, 2016 Vol.9 No.1/2, pp.25 - 53

Published online: 28 Feb 2016 *

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