title: Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks.
abstract: BACKGROUND
  Human cells of various tissue types differ greatly in morphology despite having the same set of genetic information. Some genes are expressed in all cell types to perform house-keeping functions, while some are selectively expressed to perform tissue-specific functions. In this study, we wished to elucidate how proteins encoded by human house-keeping genes and tissue-specific genes are organized in human protein-protein interaction networks. We constructed protein-protein interaction networks for different tissue types using two gene expression datasets and one protein-protein interaction database. We then calculated three network indices of topological importance, the degree, closeness, and betweenness centralities, to measure the network position of proteins encoded by house-keeping and tissue-specific genes, and quantified their local connectivity structure.
  
  
  RESULTS
  Compared to a random selection of proteins, house-keeping gene-encoded proteins tended to have a greater number of directly interacting neighbors and occupy network positions in several shortest paths of interaction between protein pairs, whereas tissue-specific gene-encoded proteins did not. In addition, house-keeping gene-encoded proteins tended to connect with other house-keeping gene-encoded proteins in all tissue types, whereas tissue-specific gene-encoded proteins also tended to connect with other tissue-specific gene-encoded proteins, but only in approximately half of the tissue types examined.
  
  
  CONCLUSIONS
  Our analysis showed that house-keeping gene-encoded proteins tend to occupy important network positions, while those encoded by tissue-specific genes do not. The biological implications of our findings were discussed and we proposed a hypothesis regarding how cells organize their protein tools in protein-protein interaction networks. Our results led us to speculate that house-keeping gene-encoded proteins might form a core in human protein-protein interaction networks, while clusters of tissue-specific gene-encoded proteins are attached to the core at more peripheral positions of the networks.
authors.affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan. heliosy@gmail.com
authors.forename: Wen-Hsien
authors.initials: WH
authors.lastname: Lin
authors.forename: Wei-Chung
authors.initials: WC
authors.lastname: Liu
authors.forename: Ming-Jing
authors.initials: MJ
authors.lastname: Hwang
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D025941:Protein Interaction Mapping; D011506:Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D011506:Proteins