title: A sub-pathway-based approach for identifying drug response principal network.
abstract: BACKGROUND
  The high redundancy of and high degree of cross-talk between biological pathways hint that a sub-pathway may respond more effectively or sensitively than the whole pathway. However, few current pathway enrichment analysis methods account for the sub-pathways or structures of the tested pathways. We present a sub-pathway-based enrichment approach for identifying a drug response principal network, which takes into consideration the quantitative structures of the pathways.
  
  
  RESULTS
  We validated this new approach on a microarray experiment that captures the transcriptional profile of dexamethasone (DEX)-treated human prostate cancer PC3 cells. Compared with GeneTrail and DAVID, our approach is more sensitive to the DEX response pathways. Specifically, not only pathways but also the principal components of sub-pathways and networks related to prostate cancer and DEX response could be identified and verified by literature retrieval.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China. chenxiujie@ems.hrbmu.edu.cn
authors.forename: Xiujie
authors.initials: X
authors.lastname: Chen
authors.forename: Jiankai
authors.initials: J
authors.lastname: Xu
authors.forename: Bangqing
authors.initials: B
authors.lastname: Huang
authors.forename: Jin
authors.initials: J
authors.lastname: Li
authors.forename: Xin
authors.initials: X
authors.lastname: Wu
authors.forename: Ling
authors.initials: L
authors.lastname: Ma
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Jia
authors.forename: Xiusen
authors.initials: X
authors.lastname: Bian
authors.forename: Fujian
authors.initials: F
authors.lastname: Tan
authors.forename: Lei
authors.initials: L
authors.lastname: Liu
authors.forename: Sheng
authors.initials: S
authors.lastname: Chen
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D045744:Cell Line, Tumor; D003907:Dexamethasone / Q000494:pharmacology; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008297:Male; D053858:Metabolic Networks and Pathways; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D025341:Principal Component Analysis; D011471:Prostatic Neoplasms / Q000188:drug therapy / Q000378:metabolism*
chemical_list: D003907:Dexamethasone