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

Q4 Pharmacology, Toxicology and Pharmaceutics
Yao Wang, Rui Wang, V. Jin
{"title":"Inference of hierarchical regulatory network of TCF7L2 binding sites in MCF7 cell line","authors":"Yao Wang, Rui Wang, V. Jin","doi":"10.1504/IJCBDD.2016.074990","DOIUrl":null,"url":null,"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.","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"9 1-2 1","pages":"25-53"},"PeriodicalIF":0.0000,"publicationDate":"2016-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2016.074990","citationCount":"2","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"International Journal of Computational Biology and Drug Design","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1504/IJCBDD.2016.074990","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"Pharmacology, Toxicology and Pharmaceutics","Score":null,"Total":0}
引用次数: 2

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.
MCF7细胞系TCF7L2结合位点分级调控网络的推断
TCF7L2转录因子(TF)是Wnt信号通路的一员,可能通过结合不同的调控区域影响多种基因的转录。全基因组研究已经确定了数千个TCF7L2结合位点,并揭示了一些相关的TF伴侣。然而,在MCF7细胞中TCF7L2及其伴生tf的分层调控网络中,仍有很大的未知区域。我们通过基于tf特定位置权重矩阵(PWM)在富集峰区域搜索基序来分析ChIP-seq数据。我们发现FOXO1和CAD与上调基因有关,AP2α、PBF和AP1与下调基因有关。TCF7L2和GATA3均与上调和下调基因相关。本研究通过挖掘MCF7细胞的ChIP-seq数据,发现了新的TCF7L2相关调控网络,这可能有助于进一步研究Wnt通路在乳腺癌或其他疾病中的相关机制。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
International Journal of Computational Biology and Drug Design
International Journal of Computational Biology and Drug Design Pharmacology, Toxicology and Pharmaceutics-Drug Discovery
CiteScore
1.00
自引率
0.00%
发文量
8
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信