ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome

Abstract : ChIP-seq experiments provide a plethora of data regarding transcription regulation in mammalian cells. Integrating ChIP-seq studies into a computable resource is potentially useful for further knowledge extraction from such data. We continually collect and expand a database where we convert results from ChIP-seq experiments into gene-set libraries. The manual portion of this database currently contains 200 transcription factors from 221 publications for a total of 458,471 transcription-factor/target interactions. In addition, we automatically compiled data from the ENCODE project which includes 920 experiments applied to 44 cell-lines profiling 160 transcription factors for a total of ~1.4 million transcription-factor/target-gene interactions. Moreover, we processed data from the NIH Epigenomics Roadmap project for 27 different types of histone marks in 64 different human cell-lines. All together the data was processed into three simple gene-set libraries where the set label is either a mammalian transcription factor or a histone modification mark in a particular cell line, organism and experiment. Such gene-set libraries are useful for elucidating the experimentally determined transcriptional networks regulating lists of genes of interest using gene-set enrichment analyses. Furthermore, from these three gene-set libraries, we constructed regulatory networks of transcription factors and histone modifications to identify groups of regulators that work together. For example, we found that the Polycomb Repressive Complex 2 (PRC2) is involved with three distinct clusters each interacting with different sets of transcription factors. Notably, the combined dataset is made into web-based application software where users can perform enrichment analyses or download the data in various formats. The open source ChEA2 web-based software and datasets are available freely online at http://amp.pharm.mssm.edu/ChEA2.
Complete list of metadatas

Cited literature [14 references]  Display  Hide  Download

https://hal.inria.fr/hal-01506771
Contributor : Hal Ifip <>
Submitted on : Wednesday, April 12, 2017 - 11:19:05 AM
Last modification on : Tuesday, August 13, 2019 - 10:56:05 AM
Long-term archiving on : Thursday, July 13, 2017 - 12:31:33 PM

File

978-3-642-40511-2_30_Chapter.p...
Files produced by the author(s)

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

  • HAL Id : hal-01506771, version 1

Citation

Yan Kou, Edward Chen, Neil Clark, Qiaonan Duan, Christopher Tan, et al.. ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. 1st Cross-Domain Conference and Workshop on Availability, Reliability, and Security in Information Systems (CD-ARES), Sep 2013, Regensburg, Germany. pp.416-430. ⟨hal-01506771⟩

Share

Metrics

Record views

270

Files downloads

306