Differential evolutionary conservation of motif modes in the yeast protein interaction network

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Lee, Wei Po ^a   Jeng, Bing Chiang ^b   Pai, Tun Wen ^c   Tsai, Chin Pei ^d   Yu, Chang Yung ^d   Tzou, Wen Shyong ^c  

^a NATIONAL UNIVERSITY OF KAOHSIUNG   (Taiwan)

^b NATIONAL SUN YAT SEN UNIVERSITY   (Taiwan)

^c NATIONAL TAIWAN OCEAN UNIVERSITY   (Taiwan)

^d PROVIDENCE UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN;

ALGORITHM; ARTICLE; CONTROLLED STUDY; GENETIC CONSERVATION; NONHUMAN; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; AMINO ACID MOTIFS; EVOLUTION, MOLECULAR; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 33746101149     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-89     Document Type: Article

References (46)

1. Glot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K. Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RLJR, White KP, Braverman M, Jarvile T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JMA: A protein interaction map of Drosophila melanogaster. Science 2003, 302:1727-1736.
2. Schwikowski B, Uetz P, Fields S: A network of protein-protein interactions in yeast. Not Biotechnol 2000, 18:1257-1261.
3. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vilayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627.
4. Walhout AJ, Boulton SJ, Vidal M: Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 2000, 17:88-94.
5. Xenarios I, Eisenberg D: Protein Interaction databases. Curr Opin Biotechnol 2001, 12:334-339.
6. Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
7. Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature 2001, 411:41-42.
8. Wagner A: The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 2001, 18:1283-1292.
9. Yook SH, Oltvai ZN, Barabasi AL: Functional and topological characterization of protein interaction networks. Proteomics; 2004, 4:928-942.
10. Wuchty S: Interaction and domain networks of yeast. Proteomics 2002, 2:1715-1723.
11. Qin H, Lu HH, Wu WB, Li WH: Evolution of the yeast protein interaction network. Proc Natl Acad Sci U S A 2003, 100:12820-12824.
12. Wagner A: Does selection mold molecular networks? Sci STKE 2003, 2003:E41.
13. Albert R, Jeong H, Barabasi AL: Error and attack tolerance of complex networks. Nature 2000, 406:378-382.
14. Fraser HB, Wall DP, Hirsh AE: A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol 2003, 3:11.
15. Fraser HB, Hirsh AF, Steinmetz LM, Scharfe C, Feldman MW: Evolutionary rate in the protein interaction network. Science 2002, 296:750-752.
16. Hahn MW, Conant GC, Wagner A. Molecular evolution in large genetic networks: does connectivity equal constraint? J Mol Evol 2004, 58:203-211.
17. Guelzim N, Bottani S, Bourgine P, Kepes F: Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 2002, 31:60-63.
18. 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.
19. Shen-Orr SS, Milo R, Mangan S, Alon U: Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002, 31:64-68.
20. Wall MF, Dunlop MJ, Hlavacek WS: Multiple functions of a feed-forward-loop gene circuit. J Mol Biol 2005, 349:501-514.
21. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804.
22. Wuchty S, Oltvai ZN, Barabasi AL: Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet 2003, 35:176-179.
23. 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 U S A 2004, 101:5934-5939.
24. Mangan S, Alon U: Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 2003, 100:11980-11985.
25. GO Database [http://www.geneontology.org/.]
26. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M: Annotation transfer between genomes: protein-protein Interologs; and protein-DNA regulogs. Genome Res 2004, 14:1107-1118.
27. Wuchty S, Barabasi AL, Ferdig MT: Stable evolutionary signal in a Yeast protein interaction network. BMC Evol Biol 2006, 6:8.
28. Vazquez A, Dobrin R, Sergi D, Eckmann JP, Oltvai ZN, Barabasi AL: The topological relationship between the large-scale attributes and local interaction patterns of complex networks. Proc Natl Acad Sci U S A 2004, 101:17940-17945.
29. Vazquez A, Oliveira JG, Barabasi AL: Inhomogeneous evolution of subgraphs and cycles in complex networks. Phys Rev E Stat Nonlin Soft Matter Phys 2005, 71:025103.
30. Breitkreutz BJ, Stark C, Tyers M: Osprey: a network visualization system. Genome Biol 2003, 4:R22.
31. de Lichtenberg U, Jensen LJ, Brunak S, Bork P: Dynamic complex formation during the yeast cell cycle. Science 2005, 307:724-727.
32. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M: Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430:88-93.
33. 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.
34. Dunn R, Dudbridge F, Sanderson CM: The use of edge-between-ness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics 2005, 6:39.
35. Rives AW, Galitski T: Modular organization of cellular networks. Proc Natl Acad Sci U S A 2003, 100:1128-1133.
36. Pereira-Leal JB, Enright AJ, Ouzounis CA: Detection of functional modules from protein Interaction networks. Proteins 2004, 54:49-57.
37. Ma HW, Zhao XM, Yuan YJ, Zeng AP: Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics 2004, 20:1870-1876.
38. Poyatos JF, Hurst LD: How biologically relevant are interaction-based modules in protein networks? Genome Biol 2004, 5:R93.
39. Spirin V, Mirny LA: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 2003, 100:12123-12128.
40. 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.
41. Kelley BP, Yuan B, Lewitter F, Sharan P, Stockwell BR, Ideker T: PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res 2004, 32:W83-W88.
42. 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.
43. Schreiber F, Schwobbermeyer H: MAVisto: a tool for the exploration of network motifs. Bioinformatics 2005, 21:3572-3574.
44. Wernicke S, Rasche F: FANMOD: a tool for fast network motif detection. Bioinformatics 2006.
45. DIP database [http://dip.doe-mbi.ucla.edu/]
46. InParanoid [http://inparanoid.cgb.ki.se/index.html]