title: Evidence for systems-level molecular mechanisms of tumorigenesis.
abstract: BACKGROUND
  Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth.
  
  
  RESULTS
  Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs") defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree) and global (betweenness and closeness) measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis.
  
  
  CONCLUSIONS
  Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins.
authors.affiliation: Bioinformatics and Biostatistics Unit, and Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Barcelona, Spain. phgutierrez@ico.scs.es <phgutierrez@ico.scs.es>
authors.forename: Pilar
authors.initials: P
authors.lastname: Hernández
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.forename: David
authors.initials: D
authors.lastname: Montaner
authors.forename: Fátima
authors.initials: F
authors.lastname: Al-Shahrour
authors.forename: Joan
authors.initials: J
authors.lastname: Valls
authors.forename: Laia
authors.initials: L
authors.lastname: Gómez
authors.forename: Gabriel
authors.initials: G
authors.lastname: Capellá
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
authors.forename: Miguel Angel
authors.initials: MA
authors.lastname: Pujana
mesh_terms: D002471:Cell Transformation, Neoplastic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D009363:Neoplasm Proteins / Q000502:physiology*; D009369:Neoplasms / Q000209:etiology / Q000235:genetics*; D011471:Prostatic Neoplasms / Q000235:genetics; D025941:Protein Interaction Mapping; D012333:RNA, Messenger / Q000378:metabolism; D015398:Signal Transduction; D049490:Systems Biology
chemical_list: D009363:Neoplasm Proteins; D012333:RNA, Messenger