%0 Conference Proceedings
%T ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome
%+ Department of pharmacology and systems therapeutics [Mount Sinai]
%A Kou, Yan
%A Chen, Edward, Y.
%A Clark, Neil, R.
%A Duan, Qiaonan
%A Tan, Christopher, M.
%A Ma‘ayan, Avi
%Z Part 1: Cross-Domain Conference and Workshop on Multidisciplinary Research and Practice for Information Systems (CD-ARES 2013)
%< avec comité de lecture
%( Lecture Notes in Computer Science
%B 1st Cross-Domain Conference and Workshop on Availability, Reliability, and Security in Information Systems (CD-ARES)
%C Regensburg, Germany
%Y Alfredo Cuzzocrea
%Y Christian Kittl
%Y Dimitris E. Simos
%Y Edgar Weippl
%Y Lida Xu
%I Springer
%3 Availability, Reliability, and Security in Information Systems and HCI
%V LNCS-8127
%P 416-430
%8 2013-09-02
%D 2013
%K ChIP-seq
%K ChIP-chip
%K Microarrays
%K Systems Biology
%K ENCODE
%K Enrichment Analysis
%K Transcriptional Networks
%K Data Integration
%K Data Visualization
%K JavaScript D3
%Z Computer Science [cs]
%Z Humanities and Social Sciences/Library and information sciencesConference papers
%X 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.
%G English
%2 https://inria.hal.science/hal-01506771/document
%2 https://inria.hal.science/hal-01506771/file/978-3-642-40511-2_30_Chapter.pdf
%L hal-01506771
%U https://inria.hal.science/hal-01506771
%~ SHS
%~ IFIP-LNCS
%~ IFIP
%~ IFIP-TC
%~ IFIP-TC5
%~ IFIP-WG
%~ IFIP-TC8
%~ IFIP-CD-ARES
%~ IFIP-WG8-4
%~ IFIP-WG8-9
%~ IFIP-LNCS-8127