Stratus not altocumulus: A new view of the yeast protein interaction network

PLoS Biology

Volumn 4, Issue 10, 2006, Pages 1720-1731

  Batada, Nizar N ^a,b   Reguly, Teresa ^a   Breitkreutz, Ashton ^a   Boucher, Lorrie ^a,c   Breitkreutz, Bobby Joe ^a   Hurst, Laurence D ^b   Tyers, Mike ^a,c  

^a MOUNT SINAI HOSPITAL   (Canada)

^b University of Bath   (United Kingdom)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; PROTEIN HUB; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; NONHUMAN; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; SACCHAROMYCES CEREVISIAE; STRUCTURE ANALYSIS; YEAST; BIOLOGICAL MODEL; BIOLOGY; COMPUTER LANGUAGE; ENTROPY; FACTUAL DATABASE; FUNGAL GENE; GENE DELETION; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; PHYSIOLOGY; PROTEIN ANALYSIS;

GOSSYPIUM HIRSUTUM; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; ENTROPY; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; GENE DELETION; GENES, FUNGAL; MODELS, GENETIC; PROGRAMMING LANGUAGES; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE;

EID: 33750238153     PISSN: 15457885     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0040317     Document Type: Article

References (53)

1. Barabasi AL, Oltvai ZN (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
2. Papp B, Pal C, Hurst LD (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429: 661-664.
3. Murray AW (2000) Whither genomics? Genome Biol 1: COMMENT003.
4. Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2.
5. Spirin V, Mirny LA (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100: 12123-12128.
6. Rives AW, Galitski T (2003) Modular organization of cellular networks. Proc Natl Acad Sci U S A 100: 1128-1133.
7. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: Simple building blocks of complex networks. Science 298: 824-827.
8. Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.
9. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402: C47-C52.
10. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
11. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
12. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-637.
13. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-644.
14. Stelling J (2004) Mathematical models in microbial systems biology. Curr Opin Microbiol 7: 513-518.
15. von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, et al. (2003) Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A 100: 15428-15433.
16. Maslov S, Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296: 910-913.
17. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
18. Aloy P, Russell RB (2002) Potential artefacts in protein-interaction networks. FEBS Lett 530: 253-254.
19. Coulomb S, Bauer M, Bernard D, Marsolier-Kergoat MC (2005) Gene essentiality and the topology of protein interaction networks. Proc Biol Sci 272: 1721-1725.
20. Maslov S, Sneppen K (2002) Protein interaction networks beyond artifacts. FEBS Lett 530: 255-256.
21. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569-4574.
22. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
23. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, et al. (2000) DIP: The database of interacting proteins. Nucleic Acids Res 28: 289-291.
24. Pereira-Leal JB, Audit B, Peregrin-Alvarez JM, Ouzounis CA (2005) An exponential core in the heart of the yeast protein interaction network. Mol Biol Evol 22: 421-425.
25. Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, et al. (2006) Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol 5: 11.
26. Batada NN, Shepp LA, Siegmund DO (2004) Stochastic model of protein-protein interaction: why signaling proteins need to be colocalized. Proc Natl Acad Sci U S A 101: 6445-6449.
27. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425: 686-691.
28. Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, et al. (2003) Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts using DNA microarray analysis. Proc Natl Acad Sci U S A 100: 11429-11434.
29. Tanaka R, Yi TM, Doyle J (2005) Some protein interaction data do not exhibit power law statistics. FEBS Lett 579: 5140-5144.
30. Bader GD, Betel D, Hogue CW (2003) BIND: The Biomolecular Interaction Network Database. Nucleic Acids Res 31: 248-250.
31. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, et al. (2002) MINT: A Molecular INTeraction database. FEBS Lett 513: 135-140.
32. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, et al. (2002) MIPS: A database for genomes and protein sequences. Nucleic Acids Res 30: 31-34.
33. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, et al. (2000) 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 U S A 97: 1143-1147.
34. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
35. Fraser HB (2005) Modularity and evolutionary constraint on proteins. Nat Genet 37: 351-352.
36. Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382.
37. Hartigan JA, Hartigan PM (1985) The dip test for unimodality. Ann Stat 13: 70-84.
38. Hartigan PM (1985) Computation of the dip statistic to test for unimodality. Appl Stat 34: 320-325.
39. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368.
40. Tong AH, Lesage G, Bader GD, Ding H, Xu H, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303: 808-813.
41. Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, et al. (2004) A robust toolkit for functional profiling of the yeast genome. Mol Cell 16: 487-496.
42. Pal C, Papp B, Hurst LD (2001) Highly expressed genes in yeast evolve slowly. Genetics 158: 927-931.
43. Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, et al. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840-846.
44. Hirsh AE, Fraser HB, Wall DP (2005) Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol 22: 174-177.
45. Krause R, von Mering C, Bork P, Dandekar T (2004) Shared components of protein complexes - versatile building blocks or biochemical artefacts? Bioessays 26: 1333-1343.
46. Campillos M, von Mering C, Jensen LJ, Bork P (2006) Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res 16: 374-382.
47. Pal C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37: 1372-1375.
48. Batada NN, Hurst LD, Tyers M (2006) Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2: e88. DOI: 10.1371/journal.pcbi. 0020088
49. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, et al. (2006) BioGRID: A general repository for interaction datasets. Nucleic Acids Res 34: D535-539.
50. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
51. Cormen TH, Leiserson CE, Rivest RL (1990) Introduction to algorithms. Cambridge (Massachusetts): MIT Press. 1028 p.
52. Cover TM, Thomas JA (1991) Elements of information theory. New York: Wiley. 542 p.
53. Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.