title: Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties.
abstract: Housekeeping genes are genes that are turned on most of the time in almost every tissue to maintain cellular functions. Tissue-selective genes are predominantly expressed in one or a few biologically relevant tissue types. Benefitting from the massive gene expression microarray data obtained over the past decades, the properties of housekeeping and tissue-selective genes can now be investigated on a large-scale manner. In this study, we analyzed the topological properties of housekeeping and tissue-selective genes in the protein-protein interaction (PPI) network. Furthermore, we compared the biological properties and amino acid usage between these two gene groups. The results indicated that there were significant differences in topological properties between housekeeping and tissue-selective genes in the PPI network, and housekeeping genes had higher centrality properties and may play important roles in the complex biological network environment. We also found that there were significant differences in multiple biological properties and many amino acid compositions. The functional genes enrichment and subcellular localizations analysis was also performed to investigate the characterization of housekeeping and tissue-selective genes. The results indicated that the two gene groups showed significant different enrichment in drug targets, disease genes and toxin targets, and located in different subcellular localizations. At last, the discriminations between the properties of two gene groups were measured by the F-score, and expression stage had the most discriminative index in all properties. These findings may elucidate the biological mechanisms for understanding housekeeping and tissue-selective genes and may contribute to better annotate housekeeping and tissue-selective genes in other organisms.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Yang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Shiyuan
authors.initials: S
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Zhou
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Chen
authors.affiliation: The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China.
authors.forename: Yongchun
authors.initials: Y
authors.lastname: Zuo
authors.affiliation: Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China. hrbmusdj@163.com.
authors.forename: Dianjun
authors.initials: D
authors.lastname: Sun
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China. lvyingli_hmu@163.com.
authors.forename: Yingli
authors.initials: Y
authors.lastname: Lv
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D020043:Genes, Essential; D006801:Humans; D009928:Organ Specificity; D060066:Protein Interaction Maps
keywords: Biological properties; Housekeeping genes; Protein interaction network; Tissue-selective genes