Generating confidence intervals on biological networks

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Thorne, Thomas ^a   Stumpf, Michael P H ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INFORMATION; BIOLOGICAL NETWORKS; BIOLOGICAL ORGANIZATION; EFFICIENT CONSTRUCTION; PROTEIN INTERACTION NETWORKS; RE-SAMPLING APPROACH; STATISTICAL APPROACH; STATISTICAL SIGNIFICANCE;

ACTIVE NETWORKS; PROTEINS; YEAST;

SAMPLING;

SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; BIOINFORMATICS; CONFIDENCE INTERVAL; CONTROLLED STUDY; CORRELATION FUNCTION; FUNGAL GENETICS; INTERMETHOD COMPARISON; NONHUMAN; PROTEIN EXPRESSION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; QUALITATIVE ANALYSIS; SACCHAROMYCES CEREVISIAE; STATISTICAL MODEL; STATISTICAL SIGNIFICANCE; ARTIFICIAL NEURAL NETWORK; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPUTER SIMULATION; FUNGAL GENE; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; PROTEIN ANALYSIS; PROTEIN DATABASE; STATISTICS;

SACCHAROMYCES CEREVISIAE;

ALGORITHMS; AMINO ACID MOTIFS; CLUSTER ANALYSIS; COMPUTER SIMULATION; CONFIDENCE INTERVALS; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENES, FUNGAL; MODELS, GENETIC; MODELS, STATISTICAL; NEURAL NETWORKS (COMPUTER); PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 39149116715     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-467     Document Type: Article

References (38)

1. Tucker C Gera J Uetz P Towards an understanding of complex protein networks Trends Cell Biol 2001, 11:102-106. 10.1016/ S0962-8924(00)01902-4 11306254
2. Gavin M Bosche M Krause R Grandi P Marzioch M Schultz J Rick J Michon A Cruciat C Remor M Hofert C Schelder M Brajenovic M Ruffner H Merino A Hudak M Dickson D Rudi T Ganu V Bauch A Bastuck S Huhse B Leutwein C Heurtier M Copley R Edelmann A Querfurth E V R Drewes G Raida M Bouwmeester T Bork P Seraphin B Kuster B Neubauer G G SF Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002, 415:141-147. 10.1038/415141a 11805826
3. Luscombe N Babu M Yu H Snyder M Teichmann S Gerstein M Genomic analysis of regulatory network dynamics reveals large topological change Nature 2004, 431:308-312. 10.1038/nature02782 15372033
4. Yu H Greenbaum D Lu HX Zhu X Gerstein M Genomic analysis of essentiality within protein networks Trends Genet 2004, 20(6):227-31. 10.1016/ j.tig.2004.04.008 15145574
5. Bork P Jensen LJ von Mering C Ramani AK Lee I Marcotte EM Protein interaction networks from yeast to human Curr Opin Struct Biol 2004, 14(3):292-9. 10.1016/j.sbi.2004.05.003 15193308
6. Agrafioti I Swire J Abbott I Huntley D Butcher S Stumpf M Comparative analysis of the Saccaromyces cerevisiae and Caenorhabditis elegans protein interaction networks BMC Evolutionary Biology 2005, 5:23. 1079807 15777474 10.1186/1471-2148-5-23
7. Bader JS Chaudhuri A Rothberg JM Chant J Gaining confidence in high-throughput protein interaction networks Nat Biotechnol 2004, 22:78-85. 10.1038/nbt924 14704708
8. Stumpf M Wiuf C May R Subnets of scale-free networks are not scale-free: the sampling properties of networks Proc Natl Acad Sci USA 2005, 102:4221-4224. 555505 15767579 10.1073/pnas.0501179102
9. Fraser HB Hirsh AE Steinmetz LM Scharfe C Feldman MW Evolutionary rate in the protein interaction network Science 2002, 296(5568):750-2. 10.1126/science.1068696 11976460
10. Lemos B Meiklejohn C Hartl D Regulatory evolution across the protein interaction network Nat Genet 2004, 36(10):1059-60. 10.1038/ng1427 15378060
11. Wagner A The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes Mol Biol Evol 2001, 18(7):1283-1292. 11420367
12. Jordan IK Wolf YI Koonin EV No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly BMC Evol Biol 2003, 3:1. 140311 12515583 10.1186/1471-2148-3-1
13. Hahn MW Conant GC Wagner A Molecular evolution in large genetic networks: Does connectivity equal constraint? J Mol Evol 2004, 58(2):203-11. 10.1007/s00239-003-2544-0 15042341
14. Milo R Shen-Orr S Itzkovitz S Kashtan N Chklovskii D Alon U Network motifs: Simple building blocks of complex networks Science 2002, 298(5594):824-827. 10.1126/science.298.5594.824 12399590
15. Milo R Itzkovitz S Kashtan N Levitt R Shen-Orr S Ayzenshtat I Sheffer M Alon U Superfamilies of evolved and designed networks Science 2004, 303(5663):1538-1542. 10.1126/science.1089167 15001784
16. Berg J Lässig M Local graph alignment and motif search in biological networks Proc Natl Acad Sci USA 2004, 101(41):14689-14694. 522014 15448202 10.1073/pnas.0305199101
17. Kashtan N Itzkovitz S Milo R Alon U Topological generalizations of network motifs Phys Rev E Stat Nonlin Soft Matter Phys 2004, 70(3 Pt 1):031909. 15524551
18. http://www.yeastgenome.org
19. http://www.wormbase.org
20. http://www.flybase.org
21. Drummond D Raval A Wilke C A single determinant dominates the rate of yeast protein evolution Mol Biol Evol 2006, 23:327-337. 10.1093/molbev/ msj038 16237209
22. http://www.imperial.ac.uk/theoreticalgenomics/data-software
23. http://dip.doe-mbi.ucla.edu
24. Xenarios I Rice D Salwinski L Baron M Marcotte E Eisenberg D Dip: The database of interacting proteins Nucl Acid Res 2000, 28:289-291. 10.1093/ nar/28.1.289
25. Hermjakob H Montecchi-Palazzi L Bader G Wojcik R Salwinski L Ceol A Moore S Orchard S Sarkans U von Mering C Roechert B Poux S Jung E Mersch H Kersey P Lappe M Li Y Zeng R Rana D Nikolski M Husi H Brun C Shanker K Grant S Sander C Bork P Zhu W Pandey A Brazma A Jacq B Vidal M Sherman D Legrain P Cesareni G Xenarios L Eisenberg D Steipe B Hogue C Apweiler R The HUPOPSI's Molecular Interaction format - a community standard for the representation of protein interaction data NATURE BIOTECHNOLOGY 2004, 22(2):177-183. 10.1038/nbt926 14755292
26. Reguly T Breitkreutz A Boucher L Breitkreutz B Hon G Myers C Parsons A Friesen H Oughtred AR amd Tong Stark C Ho Y Botstein D Andrews B Boone C Troyanskya O Ideker T Dolinski K Batada N Tyers M Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae J Biol 2006, 5:11. 1561585 16762047 10.1186/jbiol36
27. FatiGO a web tool for finding significant associations of Ontology terms with groups of genes Bioinformatics 2004, 20:578-580. 10.1093/ bioinformatics/btg455 14990455
28. http://www.fatigo.org
29. Cho R Campbell M Winzeler E Steinmetz L Conway A Wodicka L Wolfsberg T Gabrielian A Landsman D Lockhart D Davies R A genome-wide transcriptional analysis of the mitotic cell cycle Mol Cell 1998, 2:65-73. 10.1016/S1097-2765(00)80114-8 9702192
30. Functional and topological characterization of protein interaction networks Proteomics 2004, 4(4):928-42. 10.1002/pmic.200300636 15048975
31. de Silva E Thorne T Ingram P Agrafioti I Swire J Wiuf C Stumpf M The effects of incomplete protein interaction data on structural and evolutionary inferences BMC Biology 2006, 4:39. 1665463 17081312 10.1186/ 1741-7007-4-39
32. Picard F Daudin JJ Schbath S Robin S Assessing the exceptionality of network motifs 2006. http://genome.jouy.inra.fr/ssb/preprint/ [Research Report]
33. Metropolis N Rosenbluth A Rosenbluth M Teller A Teller E Equation of State Calculations by Fast Computing Machines J Chem Phys 1953, 21:1087-1092. 10.1063/1.1699114
34. Ripley BD Stochastic Simulation Wiley 1987
35. Robert C Casella G Monte Carlo Statistical Methods Springer 2 2004
36. Newman M Barkema G Monte Carlo Methods in Statistical Physics Clarendon Press 1999
37. Arfken G Weber H Mathematical Methods for Physicists Academic Press 6 2005
38. http://www.r-project.org