Design principles of molecular networks revealed by global comparisons and composite motifs

Genome Biology

Volumn 7, Issue 7, 2006, Pages

  Yu, Haiyuan ^a   Xia, Yu ^a   Trifonov, Valery ^a   Gerstein, Mark ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POL PROTEIN; TATA BINDING PROTEIN; PROTEIN;

ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE MAPPING; GENETIC DISTANCE; METABOLIC REGULATION; MOLECULAR GENETICS; MOLECULAR INTERACTION; NONHUMAN; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN METABOLISM; PROTEIN MOTIF; REGULATORY MECHANISM; SEGREGATION ANALYSIS; YEAST; CHEMISTRY; PROTEIN CONFORMATION;

AMINO ACID MOTIFS; PROTEIN CONFORMATION; PROTEINS;

EID: 33747379012     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2006-7-7-r55     Document Type: Article

References (56)

1. Hartwell LH, Hopfield JJ, Leibler S, Murray AW: From molecular to modular cell biology. Nature 1999, 402(6761 Suppl):C47-52.
2. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y: Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA 2000, 97:1143-1147.
3. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, et al.: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627.
4. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, et al.: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415:141-147.
5. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, et al.: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415:180-183.
6. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, et al.: A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell 1998, 2:65-73.
7. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M: The KEGG resource for deciphering the genome. Nucleic Acids Res 2004:D277-280.
8. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, et al.: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804.
9. Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M: Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 2002, 16:3017-3033.
10. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, et al.: Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 2001, 294:2364-2368.
11. Nakaya A, Goto S, Kanehisa M: Extraction of correlated gene clusters by multiple graph comparison. Genome Inform Ser 2001, 12:44-53.
12. Albert R, Barabasi AL: Statistical mechanics of complex networks. Rev Modern Phys 2002, 74:47-97.
13. Amaral LA, Scala A, Barthelemy M, Stanley HE: Classes of small-world networks. Proc Natl Acad Sci USA 2000, 97:11149-11152.
14. Girvan M, Newman ME: Community structure in social and biological networks. Proc Natl Acad Sci USA 2002, 99:7821-7826.
15. Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature 2001, 411:41-42.
16. Yu H, Zhu X, Greenbaum D, Karro J, Gerstein M: TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Res 2004, 32:328-337.
17. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: simple building blocks of complex networks. Science 2002, 298:824-827.
18. Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H: Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci USA 2004, 101:5934-5939.
19. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M: Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312.
20. Ihmels J, Levy R, Barkal N: Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol 2004, 22:86-92.
21. Balazsi G, Barabasi AL, Oltvai ZN: Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci USA 2005, 102:7841-7846.
22. Guelzim N, Bottani S, Bourgine P, Kepes F: Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 2002, 31:60-63.
23. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW: Evolutionary rate in the protein interaction network. Science 2002, 296:750-752.
24. Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M: Genomic analysis of essentiality within protein networks. Trends Genet 2004, 20:227-231.
25. Hinnebusch AG, Natarajan K: Gcn4p, a master regulator of gene expression, is controlled at multiple levels by diverse signals of starvation and stress. Eukaryot Cell 2002, 1:22-32.
26. Drysdale CM, Duenas E, Jackson BM, Reusser U, Braus GH, Hinnebusch AG: The transcriptional activator GCN4 contains multiple activation domains that are critically dependent on hydrophobic amino acids. Mol Cell Biol 1995, 15:1220-1233.
27. Ge H, Liu Z, Church GM, Vidal M: Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 2001, 29:482-486.
28. Grigoriev A: A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2001, 29:3513-3519.
29. Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC: Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell 2002, 9:1133-1143.
30. Jansen R, Greenbaum D, Gerstein M: Relating whole-genome expression data with protein-protein interactions. Genome Res 2002, 12:37-46.
31. Yu H, Luscombe NM, Qian J, Gerstein M: Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet 2003, 19:422-427.
32. Shen-Orr SS, Milo R, Mangan S, Alon U: Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics 2002, 31:64-68.
33. Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U: Just-in-time transcription program in metabolic pathways. Nat Genet 2004, 36:486-491.
34. Kalir S, Alon U: Using a quantitative blueprint to reprogram the dynamics of the flagella gene network. Cell 2004, 117:713-720.
35. Basu S, Mehreja R, Thiberge S, Chen MT, Weiss R: Spatiotemporal control of gene expression with pulse-generating networks. Proc Natl Acad Sci USA 2004, 101:6355-6360.
36. Mangan S, Alon U: Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 2003, 100:11980-11985.
37. Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M, Brown P, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297.
38. Mazurie A, Bottani S, Vergassola M: An evolutionary and functional assessment of regulatory network motifs. Genome Biol 2005, 6:R35.
39. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhauser R, et al.: The TRANSFAC system on gene expression regulation. Nucleic Acids Res 2001, 29:281-283.
40. Hodges PE, McKee AH, Davis BP, Payne WE, Garrels JI: The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Res 1999, 27:69-73.
41. Bader GD, Betel D, Hogue CW: BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 2003, 31:248-250.
42. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B: MIPS: a database for genomes and protein sequences. Nucleic Acids Res 2002, 30:31-34.
43. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D: DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30:303-305.
44. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403.
45. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302:449-453.
46. Supplementary Data Website [http://networks.gersteinlab.org/network/ netcomp/]
47. Zhang LV, King OD, Wong SL, Goldberg DS, Tong AH, Lesage G, Andrews B, Bussey H, Boone C, Roth FP: Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol 2005, 4:6.
48. Qian J, Dolled-Filhart M, Lin J, Yu H, Gerstein M: Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J Mol Biol 2001, 314:1053-1066.
49. Cupp JR, McAlister-Henn L: Kinetic analysis of NAD(+)-isocitrate dehydrogenase with altered isocitrate binding sites: contribution of IDH1 and IDH2 subunits to regulation and catalysis. Biochemistry 1993, 32:9323-9328.
50. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409:533-538.
51. Daignan-Fornier B, Fink GR: Coregulation of purine and histidine biosynthesis by the transcriptional activators BAS1 and BAS2. Proc Natl Acad Sci USA 1992, 89:6746-6750.
52. Dirick L, Bohm T, Nasmyth K: Roles and regulation of Cln-Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. EMBO J 1995, 14:4803-4813.
53. Machado AK, Morgan BA, Merrill GF: Thioredoxin reductase-dependent inhibition of MCB cell cycle box activity in Saccharomyces cerevisiae. J Biol Chem 1997, 272:17045-17054.
54. Matangkasombut O, Buratowski S: Different sentitivities of bromodomain factors 1 and 2 to histone H4 acetylation. Mol Cell 2003, 11:353-363.
55. Miyoshi K, Shirai C, Mizuta K: Transcription of genes encoding trans-acting factors required for rRNA maturation/ribosomal subunit assembly is coordinately regulated with ribosomal protein genes and involves Rap1 in Saccharomyces cerevisiae. Nucleic Acids Res 2003, 31:1969-1973.
56. Ogawa N, Noguchi K, Sawai H, Yamashita Y, Yompakdee C, Oshima Y: Functional domains of Pho81p, an inhibitor of Pho85p protein kinase, in the transduction pathway of Pi signals in Saccharomyces cerevisiae. Mol Cell Biol 1995, 15:997-1004.