Volume 7 Number 12 (Dec. 2012)
Home > Archive > 2012 > Volume 7 Number 12 (Dec. 2012) >
JSW 2012 Vol.7(12): 2755-2762 ISSN: 1796-217X
doi: 10.4304//jsw.7.12.2755-2762

Analyzing ChIP-seq Data based on Multiple Knowledge Sources for Histone Modification

Dafeng Chen1, Deyu Zhou2, Yuliang Zhuang1
1School of Information Science, Nanjing Audit University, Nanjing 211815, China
2School of Computer Science and Engineering, Southeast University, Nanjing 210029, China

Abstract—ChIP-seq is able to capture the genomic profiles for histone modification by combining chromatin immunoprecipitation (ChIP) with next generation sequencing. However, enriched regions generated from peak finding algorithms are evaluated only based on the limited knowledge acquired from manually examining the relevant biological literature. This paper proposes a novel framework of incorporating multiple knowledge sources, consisting of information extracted from biological literature, Gene Ontology, and microarray data, in order to precisely analyze ChIP-seq data for histone modification. The information is combined in a unified probabilistic model to rerank the enriched regions generated from peak finding algorithms. Through filtering the reranked enriched regions using some predefined threshold, more reliable and precise results could be generated. The combination of the multiple knowledge sources with the peaking finding algorithm produces a new paradigm for ChIP-seq data analysis.

Index Terms—ChIP-seq, histone modification, reranking, information extraction

[PDF]

Cite: Dafeng Chen, Deyu Zhou, Yuliang Zhuang, "Analyzing ChIP-seq Data based on Multiple Knowledge Sources for Histone Modification," Journal of Software vol. 7, no. 12, pp. 2755-2762, 2012.

General Information

ISSN: 1796-217X (Online)
Frequency: Monthly
Editor-in-Chief: Prof. Antanas Verikas
Executive Editor: Ms. Yoyo Y. Zhou
Abstracting/ Indexing: DBLP, EBSCO, ProQuest, INSPEC, ULRICH's Periodicals Directory, WorldCat, etc
E-mail: jsw@iap.org
  • Dec 06, 2019 News!

    Vol 14, No 1- Vol 14, No 4 has been indexed by EI (Inspec)   [Click]

  • Nov 18, 2019 News!

    Papers published in JSW Vol 14, No 1- Vol 14 No 10 have been indexed by DBLP     [Click]

  • Dec 06, 2019 News!

     Vol 13, No 10- Vol 13, No 12 has been indexed by EI (Inspec)   [Click]

  • Aug 01, 2018 News!

    [CFP] 2020 the annual meeting of JSW Editorial Board, ICCSM 2020, will be held in Rome, Italy, July 17-19, 2020   [Click]

  • Jun 25, 2019 News!

    Vol.13, No.9 has been indexed by EI (Inspec).   [Click]