title: The network organization of cancer-associated protein complexes in human tissues.
abstract: Differential gene expression profiles for detecting disease genes have been studied intensively in systems biology. However, it is known that various biological functions achieved by proteins follow from the ability of the protein to form complexes by physically binding to each other. In other words, the functional units are often protein complexes rather than individual proteins. Thus, we seek to replace the perspective of disease-related genes by disease-related complexes, exemplifying with data on 39 human solid tissue cancers and their original normal tissues. To obtain the differential abundance levels of protein complexes, we apply an optimization algorithm to genome-wide differential expression data. From the differential abundance of complexes, we extract tissue- and cancer-selective complexes, and investigate their relevance to cancer. The method is supported by a clustering tendency of bipartite cancer-complex relationships, as well as a more concrete and realistic approach to disease-related proteomics.
authors.affiliation: Department of Mathematics, Logistical Engineering University, Chongqing, China. zhaojanne@gmail.com
authors.forename: Jing
authors.initials: J
authors.lastname: Zhao
authors.forename: Sang Hoon
authors.initials: SH
authors.lastname: Lee
authors.forename: Mikael
authors.initials: M
authors.lastname: Huss
authors.forename: Petter
authors.initials: P
authors.lastname: Holme
mesh_terms: D000465:Algorithms; D001932:Brain Neoplasms / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008954:Models, Biological; D046912:Multiprotein Complexes / Q000378:metabolism*; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D040901:Proteomics / Q000379:methods; D015203:Reproducibility of Results
chemical_list: D046912:Multiprotein Complexes