A network-based gene-weighting approach for pathway analysis

	A network-based gene-weighting approach for pathway analysis
	Fang, ZY; Tian, WD; Ji, HB
刊名	CELL RESEARCH
	2012
卷号	22 期号:3 页码:565-580
关键词	gene weighting functional association network pathway analysis gene set analysis gene expression microarray multi-subunit protein
通讯作者	Ji, HB (reprint author), Chinese Acad Sci, Inst Biochem & Cell Biol, State Key Lab Cell Biol, SIBS, Shanghai 200031, Peoples R China.,weidong.tian@fudan.edu.cn ; hbji@sibs.ac.cn
英文摘要	Classical algorithms aiming at identifying biological pathways significantly related to studying conditions frequently reduced pathways to gene sets, with an obvious ignorance of the constitutive non-equivalence of various genes within a defined pathway. We here designed a network-based method to determine such non-equivalence in terms of gene weights. The gene weights determined are biologically consistent and robust to network perturbations. By integrating the gene weights into the classical gene set analysis, with a subsequent correction for the "over-counting" bias associated with multi-subunit proteins, we have developed a novel gene-weighed pathway analysis approach, as implemented in an R package called "Gene Associaqtion Network-based Pathway Analysis" (GANPA). Through analysis of several microarray datasets, including the p53 dataset, asthma dataset and three breast cancer datasets, we demonstrated that our approach is biologically reliable and reproducible, and therefore helpful for microarray data interpretation and hypothesis generation.
学科主题	Cell Biology
类目[WOS]	Cell Biology
关键词[WOS]	ENDOTHELIAL GROWTH-FACTOR ; WIDE EXPRESSION PROFILES ; PROBE LEVEL DATA ; SET ENRICHMENT ; TESTING ASSOCIATION ; BIOLOGICAL PATHWAYS ; GLOBAL TEST ; CELL-CYCLE ; CANCER ; IDENTIFICATION
收录类别	SCI
语种	英语
WOS记录号	WOS:000300942400013
内容类型	期刊论文
版本	出版稿
源URL	[http://202.127.25.143/handle/331003/561]
专题	上海生化细胞研究所_上海生科院生化细胞研究所
推荐引用方式 GB/T 7714	Fang, ZY,Tian, WD,Ji, HB. A network-based gene-weighting approach for pathway analysis[J]. CELL RESEARCH,2012,22(3):565-580.
APA	Fang, ZY,Tian, WD,&Ji, HB.(2012).A network-based gene-weighting approach for pathway analysis.CELL RESEARCH,22(3),565-580.
MLA	Fang, ZY,et al."A network-based gene-weighting approach for pathway analysis".CELL RESEARCH 22.3(2012):565-580.