Genomics

Dataset Information

298

Genome-wide maps of Tamoxifen resistance MCF7 cell line


ABSTRACT: We report the ER alpha regulatory network of Tamoxifen resistance MCF7 cell line using the Chromatin immunoprecipitated high-throughput sequencing technology (ChIP-seq). By Integrating the gene expression data (previously reported) with the ChIP-seq data, we generated ER alpha regulatory network and pathways. For ER alpha regulatory network, hub TFs with enriched motifs were identified from ER alpha peak together with PolII peaks. We then scan the position weight matrix (PWM) of ER alpha peak region of certain gene to find out the regulatory relationship between hub TF and normal TF. For regulatory pathway, genes were grouped base on their expression value at 4 different time point. Then the hub TF that plays important role in each time point of each group was identified. This study provides a framework for the application of ChIP-seq and gene expression data for the construction of ER alpha regulatory network. 4 different ChIP-seq dataset in Tamoxifen resistance MCF7 cell line

ORGANISM(S): Homo sapiens  

SUBMITTER: Victor X Jin   Jeffrey Parvin  Pei-Yin Hsu  Fei Gu  Tim H Huang  Hang-Kai Hsu  Jiejun Wu  Yilin Ma 

PROVIDER: E-GEOD-26083 | ArrayExpress | 2010-12-20

SECONDARY ACCESSION(S): SRP004916GSE26083PRJNA135221

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data.

Gu Fei F   Hsu Hang-Kai HK   Hsu Pei-Yin PY   Wu Jiejun J   Ma Yilin Y   Parvin Jeffrey J   Huang Tim H-M TH   Jin Victor X VX  

BMC systems biology 20101217


Global profiling of in vivo protein-DNA interactions using ChIP-based technologies has evolved rapidly in recent years. Although many genome-wide studies have identified thousands of ERα binding sites and have revealed the associated transcription factor (TF) partners, such as AP1, FOXA1 and CEBP, little is known about ERα associated hierarchical transcriptional regulatory networks.In this study, we applied computational approaches to analyze three public available ChIP-based datasets: ChIP-seq,  ...[more]

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