title: Attractors of hypertrophic cardiomyopathy using maximal cliques and attract methods.
abstract: BACKGROUND
  Our study was designed to identify the differential attractor modules related with hypertrophic cardiomyopathy (HCM) by integrating clustering-based on maximal cliques algorithm and Attract method.
  
  
  METHODS
  We firstly recruited the HCM-related microarray data from ArrayExpress database. Next, protein-protein interaction (PPI) networks of normal and HCM were constructed and re-weighted using spearman correlation coefficient (SCC). Then, maximal cliques were found from the PPI networks through the clustering-based on maximal cliques approach. Afterwards, highly overlapped cliques were eliminated or merged according to the interconnectivity, and then modules were obtained. Subsequently, we used Attract method to identify differential attractor modules, following by the pathway enrichment analyses for genes in differential attractor modules.
  
  
  RESULTS
  After removing the cliques with nodes less than or equal to 4, 926 and 1118 maximal cliques in normal and HCM PPI networks were obtained for module analysis. Then, we obtained 32 and 55 modules from the PPI networks of normal and HCM, respectively. By comparing with normal condition, there were 5 module pairs with the same or similar gene composition. Significantly, based on attract method, we found that these 5 modules were differential attractors. Pathway enrichment analyses indicated that proteasome, ribosome and oxidative phosphorylation were the significant pathways.
  
  
  CONCLUSIONS
  Proteasome, ribosome and oxidative phosphorylation might play pathophysiological roles in HCM.
authors.affiliation: Department of Cardiology, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China. Electronic address: fengmingjunhos@163.com.
authors.forename: Ming-Jun
authors.initials: MJ
authors.lastname: Feng
authors.affiliation: Department of Cardiology, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China. Electronic address: chuhuiminhang@163.com.
authors.forename: Hui-Min
authors.initials: HM
authors.lastname: Chu
authors.affiliation: Department of Cardiology, Ningbo Seventh Hospital, Ningbo 315000, Zhejiang Province, China. Electronic address: nbscj198510@163.com.
authors.forename: Cai-Jie
authors.initials: CJ
authors.lastname: Shen
authors.affiliation: Department of Cardiology, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China. Electronic address: hebinbinedu@163.com.
authors.forename: Bin
authors.initials: B
authors.lastname: He
authors.affiliation: Department of Cardiology, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China. Electronic address: duxianfengmed@sina.com.
authors.forename: Xian-Feng
authors.initials: XF
authors.lastname: Du
authors.affiliation: Department of Cardiology, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China. Electronic address: yuyiboai@sina.com.
authors.forename: Yi-Bo
authors.initials: YB
authors.lastname: Yu
authors.affiliation: Department of Cardiology, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China. Electronic address: liujingfirsthos@sina.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Cardiology, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China. Electronic address: cxmfriend@sina.com.
authors.forename: Xiao-Min
authors.initials: XM
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D002312:Cardiomyopathy, Hypertrophic / Q000209:etiology* / Q000235:genetics*; D042967:Electron Transport Complex I / Q000235:genetics; D006801:Humans; D046228:Microarray Analysis / Q000379:methods; D046988:Proteasome Endopeptidase Complex / Q000235:genetics; D060066:Protein Interaction Maps / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics
chemical_list: D012269:Ribosomal Proteins; D046988:Proteasome Endopeptidase Complex; D042967:Electron Transport Complex I
keywords: Attract; Attractor modules; Hypertrophic cardiomyopathy; Module correlation density; Pathways