Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes

Human Molecular Genetics

Volumn 15, Issue 8, 2006, Pages 1313-1318

  Liu, Song ^a   Zhang, Chi ^a   Zhou, Yaoqi ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BRAIN; CENTRAL NERVOUS SYSTEM; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE NUMBER; GENE STRUCTURE; GENETIC CODE; GENOME SIZE; HOUSEKEEPING GENE; INTRON; MOUSE; NONHUMAN; PRIORITY JOURNAL; TISSUE SPECIFICITY;

MAMMALIA;

EID: 33645799477     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddl051     Document Type: Article

References (27)

1. Vinogradov, A.E. (2004). Evolution of genome size: Multilevel selection, mutation bias or dynamical chaos? Curr. Opin. Genet. Dev., 14, 620-626.
2. Castillo-Davis, C.I., Mekhedov, S.L., Hartl, D.L., Koonin, E.V. and Kondrashov, F.A. (2002). Selection for short introns in highly expressed genes. Nat. Genet., 31, 415-418.
3. Urrutia, A.O. and Hurst, L.D. (2003). The signature of selection mediated by expression on human genes. Genome Res., 13, 2260-2264.
4. Eisenberg, E. and Levanon, E.Y. (2003). Human housekeeping genes are compact. Trends Genet., 19, 362-365.
5. Vinogradov, A.E. (2004). Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet., 20, 248-253.
6. Lehner, B. and Fraser, A.G. (2004). Protein domains enriched in mammalian tissue-specific or widely expressed genes. Trends Genet., 20, 468-472.
7. Cohen-Gihon, I., Lancet, D. and Yanai, I. (2005). Modular genes with metazoan-specific domains have increased tissue specificity. Trends Genet., 21, 210-213.
8. Farh, K.K.-H., Grimson, A., Jan, C., Lewis, B.P., Johnston, W.K., Lim, L.P., Burge, C.B. and Bartel, D.P. (2005). The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science, 310, 1817-1821.
9. Zhang, W., Morris, Q.D., Chang, R., Shai, O., Bakowskil, M.A., Mitsakakis, N., Mohammad, N., Robinson, M.D., Zirngibl, R. Somogyi E. et al. (2004). The functional landscape of mouse gene expression. J. Biol., 3, 21.
10. Jonathan, B.W. (2004). Co-regulation of mouse genes predicts function. J. Biol., 3, 19.
11. Holmes, C. and Brown, S.D. (2004). All systems go for understanding mouse gene function. J. Biol., 3, 20.
12. Jordan, I.K., Mario-Ramrez, L., Wolf, Y.I. and Koonin, E.V. (2004). Conservation and coevolution in the scale-free human gene coexpression network. Mol. Biol. Evol., 21, 2058-2070.
13. Basso, K., Margolin, A.A., Stolovitzky, G., Klein, U., Dalla-Favera, R. and Califano, A. (2005). Reverse engineering of regulatory networks in human B cells. Nat. Genet., 37, 382-390.
14. Petti, A.A. and Church, G.M. (2005). A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Res., 15, 1298-1306.
15. Barabasi, A.L. and Oltvai, Z.N. (2004). Network biology: Understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-113.
16. Xia, Y., Yu, H., Jansen, R., Seringhaus, M., Baxter, S., Greenbaum, D., Zhao, H. and Gerstein, M. (2004). Analyzing cellular biochemistry in terms of molecular networks. Annu. Rev. Biochem., 73, 1051-1087.
17. Fraser, H.B., Hirsh, A.E., Steinmetz, L.M., Scharfe, C. and Feldman, M.W. (2002). Evolutionary rate in the protein interaction network. Science, 296, 750-752.
18. Yu, H., Greenbaum, D., Lu, H.X., Zhu, X. and Gerstein, M. (2004). Genomic analysis of essentiality within protein networks. Trends Genet., 20, 227-231.
19. Luscombe, N.M., Babu, M.M., Yu, H., Snyder, M., Teichmann, S.A. and Gerstein, M. (2004). Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431, 308-312.
20. Babu, M.M., Luscombe, N.M., Aravind, L., Gerstein, M. and Teichmann, S.A. (2004). Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol., 14, 283-291.
21. Ge, H., Liu, Z., Church, G.M. and Vida, M. (2001). Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet., 29, 482-486.
22. Gunsalus, K.C., Ge, H., Schetter, A.J., Goldberg, D.S., Han, J.-D.J., Hao, T., Berriz, G.F., Bertin, N., Huang, J. Chuang, L.-S. et al. (2005). Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 436, 801-865.
23. Maciag, K., Altschuler, S.J., Slack, M.D., Krogan, N.J., Emili, A., Greenblatt, J.F., Maniatis, T. and Wu, L.F. (2006). Systems-level analyses identify extensive coupling among gene expression machines. Mol. Syst. Biol., msb4100045-E1.
24. Dorus, S., Vallender, E.J., Evans, P.D., Anderson, J.R., Gilbert, S.L., Mahowald, M., Wyckoff, G.J., Malcom, C.M. and Lahn, B.T. (2004). Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell, 119, 1027-1040.
25. Sironi, M., Menozzi, G., Comi, G.P., Cagliani, R., Bresolin, N. and Pozzoli, U. (2005). Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences. Hum. Mol. Genet., 14, 2533-2546.
26. Zhou, X.H., Kao, M.C.J. and Wong, W.H. (2002). Transitive functional annotation by shortest path analysis of gene expression data. Proc. Natl Acad. Sci. USA, 99, 12783-12788.
27. Zhou, X.J., Kao, M.-C.J., Huang, H., Wong, A., Nunez-Iglesias, J., Primig, M., Aparicio, O.M., Finch, C.E., Morgan, T.E. and Wong, W.H. (2005). Functional annotation and network reconstruction through cross-platform integration of microarray data. Nat. Biotechnol., 23, 238-243.