title: Principal network analysis: identification of subnetworks representing major dynamics using gene expression data.
abstract: BACKGROUND
  Systems biology attempts to describe complex systems behaviors in terms of dynamic operations of biological networks. However, there is lack of tools that can effectively decode complex network dynamics over multiple conditions.
  
  
  RESULTS
  We present principal network analysis (PNA) that can automatically capture major dynamic activation patterns over multiple conditions and then generate protein and metabolic subnetworks for the captured patterns. We first demonstrated the utility of this method by applying it to a synthetic dataset. The results showed that PNA correctly captured the subnetworks representing dynamics in the data. We further applied PNA to two time-course gene expression profiles collected from (i) MCF7 cells after treatments of HRG at multiple doses and (ii) brain samples of four strains of mice infected with two prion strains. The resulting subnetworks and their interactions revealed network dynamics associated with HRG dose-dependent regulation of cell proliferation and differentiation and early PrPSc accumulation during prion infection.
  
  
  BACKGROUND
  The web-based software is available at: http://sbm.postech.ac.kr/pna.
authors.affiliation: School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea.
authors.forename: Yongsoo
authors.initials: Y
authors.lastname: Kim
authors.forename: Taek-Kyun
authors.initials: TK
authors.lastname: Kim
authors.forename: Yungu
authors.initials: Y
authors.lastname: Kim
authors.forename: Jiho
authors.initials: J
authors.lastname: Yoo
authors.forename: Sungyong
authors.initials: S
authors.lastname: You
authors.forename: Inyoul
authors.initials: I
authors.lastname: Lee
authors.forename: George
authors.initials: G
authors.lastname: Carlson
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
authors.forename: Seungjin
authors.initials: S
authors.lastname: Choi
authors.forename: Daehee
authors.initials: D
authors.lastname: Hwang
mesh_terms: D000818:Animals; D001669:Biochemical Phenomena; D002454:Cell Differentiation / Q000187:drug effects; D002460:Cell Line; D049109:Cell Proliferation / Q000187:drug effects; D003198:Computer Simulation; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D051379:Mice; D020890:Neuregulin-1 / Q000494:pharmacology; D017096:Prion Diseases / Q000503:physiopathology; D012984:Software; D049490:Systems Biology / Q000379:methods*
chemical_list: D020890:Neuregulin-1