TY - JOUR
T1 - Knowledge integration for analyzing ChIP-seq
AU - Zhou, Deyu
AU - He, Yulan
PY - 2012
Y1 - 2012
N2 - To capture the genomic profiles for histone modification, chromatin immunoprecipitation (ChIP) is combined with next generation sequencing, which is called ChIP-seq. However, enriched regions generated from the ChIP-seq data are only evaluated on the limited knowledge acquired from manually examining the relevant biological literature. This paper proposes a novel framework, which integrates multiple knowledge sources such as biological literature, Gene Ontology, and microarray data. In order to precisely analyze ChIP-seq data for histone modification, knowledge integration is based on a unified probabilistic model. The model is employed to re-rank 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.
AB - To capture the genomic profiles for histone modification, chromatin immunoprecipitation (ChIP) is combined with next generation sequencing, which is called ChIP-seq. However, enriched regions generated from the ChIP-seq data are only evaluated on the limited knowledge acquired from manually examining the relevant biological literature. This paper proposes a novel framework, which integrates multiple knowledge sources such as biological literature, Gene Ontology, and microarray data. In order to precisely analyze ChIP-seq data for histone modification, knowledge integration is based on a unified probabilistic model. The model is employed to re-rank 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.
KW - ChIP-seq
KW - microarray
KW - knowledge integration
KW - histone modification
KW - gene ontology
UR - http://www.scopus.com/inward/record.url?scp=84868660003&partnerID=8YFLogxK
UR - http://www.scientific.net/AMR.532-533.1344
U2 - 10.4028/www.scientific.net/AMR.532-533.1344
DO - 10.4028/www.scientific.net/AMR.532-533.1344
M3 - Article
AN - SCOPUS:84868660003
SN - 1022-6680
VL - 532-533
SP - 1344
EP - 1348
JO - Advanced Materials Research
JF - Advanced Materials Research
ER -