Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data

Molecular Systems Biology

Volumn 6, Issue , 2010, Pages

  Choi, Hyungwon ^a   Kim, Sinae ^b   Gingras, Anne Claude ^c,d   Nesvizhskii, Alexey I ^a,b  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

^c MOUNT SINAI HOSPITAL   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

clustering; mass spectrometry; protein complexes; protein protein interaction; spectral counts

Indexed keywords

MULTIPROTEIN COMPLEX; PHOSPHOPROTEIN PHOSPHATASE 2A; CARRIER PROTEIN; HELICASE; PHOSPHOPROTEIN PHOSPHATASE 2; RUVBL1 PROTEIN, HUMAN; RUVBL2 PROTEIN, HUMAN;

AFFINITY PURIFICATION; ALGORITHM; ARTICLE; CLUSTER ANALYSIS; HUMAN; INTERMETHOD COMPARISON; MAMMAL CELL; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; AFFINITY CHROMATOGRAPHY; BIOLOGICAL MODEL; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEIN DATABASE; STAINING;

MAMMALIA;

CARRIER PROTEINS; CHROMATOGRAPHY, AFFINITY; CLUSTER ANALYSIS; DATABASES, PROTEIN; DNA HELICASES; HUMANS; MASS SPECTROMETRY; MODELS, BIOLOGICAL; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN PHOSPHATASE 2; STAINING AND LABELING;

EID: 77953994414     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2010.41     Document Type: Article

References (43)

1. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422: 198-207
2. Antoniak CE (1974) Mixtures of Dirichlet processes with applications to Bayesian nonparametric problems. Ann Stat 2: 1152-1174
3. Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, Yu H, Sahalie JM, Murray RR, Roncari L, de Smet AS, Venkatesan K, Rual JF, Vandenhaute J, Cusick ME, Pawson T, Hill DE, Tavernier J, Wrana JL, Roth FP, Vidal M (2009) An experimentally derived confidence score for binary protein-protein interactions. Nat Methods 6: 91-97
4. Breitkreutz A, Choi H, Sharom J, Boucher L, Neduva V, Larsen B, Lin Z-Y, Breitkreutz B-J, Stark C, Liu G,Ahn J,Dewar-Darch D, Reguly T,TangX,Almeida R, QinZS, Pawson T, GingrasA-C,Nesvizhskii AI, Tyers M (2010) Global architecture of the yeast protein kinase and phosphatase interaction network. Science 328: 1043-1046
5. Chen GI, Gingras AC (2007) Affinity-purification mass spectrometry (AP-MS) of serine/threonine phosphatases. Methods 42: 298-305
6. Cheng Y, Church GM (2000) Biclustering of expression data. Proc Int Conf Intell Syst Mol Biol 8: 93-103
7. Choi H, Fermin D, Nesvizhskii AI (2008) Significance analysis of spectral count data in label-free shotgun proteomics. Mol Cell Proteomics 7: 2373-2385
8. Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC,Weissman JS, Krogan NJ (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6: 439-450
9. Dudoit S, Fridlyand J (2002) A prediction-based resampling method for estimating the number of clusters in a dataset. Genome Biol 3: RESEARCH0036
10. Fraley C, Raftery AE (2002) Model-based clustering, discriminant analysis, and density estimation. J Am Stat Assoc 97: 611-631
11. Friedel CC, Zimmer R (2009) Identifying the topology of protein complexes from affinity purification assays. Bioinformatics 25: 2140-2146
12. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M et al (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636
13. Gingras AC, Caballero M, Zarske M, Sanchez A, Hazbun TR, Fields S, Sonenberg N, Hafen E, Raught B, Aebersold R (2005) A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity. Mol Cell Proteomics 4: 1725-1740
14. Gingras AC, Gstaiger M, Raught B, Aebersold R (2007) Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 8: 645-654
15. Glatter T, Wepf A, Aebersold R, Gstaiger M (2009) An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol 5: 237
16. Goudreault M, D'Ambrosio LM, Kean MJ, Mullin MJ, Larsen BG, Sanchez A, Chaudhry S, Chen GI, Sicheri F, Nesvizhskii AI, Aebersold R, Raught B, Gingras AC (2009) A PP2A phosphatase high density interaction network identifies a novel striatininteracting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Mol Cell Proteomics 8: 157-171
17. Hart GT, Lee I, Marcotte ER (2007) A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics 8: 236
18. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C et al (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183
19. Kim S, Tadesse MG, VannucciM(2006) Variable selection in clustering via Dirichlet process mixture models. Biometrika 93: 877-893
20. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B et al (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643
21. Lazzeroni L, Owen A (2002) Plaid models for gene expression data. Stat Sinica 12: 61-86
22. Liu H, Sadygov RG, Yates III JR (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: 4193-4201
23. Lu P, Vogel C, Wang R, Yao X, Marcotte EM (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25: 117-124
24. Nesvizhskii AI, Aebersold R (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics 4: 1419-1440
25. Nesvizhskii AI, Vitek O, Aebersold R (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4: 787-797
26. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4: 1487-1502
27. Powell DW, Weaver CM, Jennings JL, McAfee KJ, He Y, Weil PA, Link AJ (2004) Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol Cell Biol 24: 7249-7259
28. Prelic A, Bleuler S, Zimmermann P, Wille A, Buhlmann P, GruissemW, Hennig L, Thiele L, Zitzler E (2006) A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics 22: 1122-1129
29. Pu SY, Vlasblom J, Emili A, Greenblatt J, Wodak SJ (2007) Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics 7: 944-960 (Pubitemid 46506741)
30. Rodriguez A, Dunson DB, Gelfand AE (2008) The nested Dirichlet process. J Am Stat Assoc 103: 1131-1154
31. Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, Conaway JW, Florens L, Washburn MP (2008) Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci USA 105: 1454-1459
32. Sardiu ME, Florens L, Washburn MP (2009) Evaluation of clustering algorithms for protein complex and protein interaction network assembly. J Proteome Res 8: 2944-2952
33. Scholtens D, Vidal M, Gentleman R (2005) Local modeling of global interactome networks. Bioinformatics 21: 3548-3557
34. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
35. Sowa ME, Bennett EJ, Gygi SP, Harper JW (2009) Defining the human deubiquitinating enzyme interaction landscape. Cell 138: 389-403
36. Teh YW, Jordan MI, Beal MJ, Blei DM (2006) Hierarchical Dirichlet processes. J Am Stat Assoc 101: 1566-1581
37. Tibshirani R, Walther G, Hastie T (2001) Estimating the number of clusters in a dataset via the Gap statistic. J Roy Stat Soc B 63: 411-423
38. Valpuesta JM, Martin-Benito J, Gomez-Puertas P, Carrascosa JL, Willison KR (2002) Structure and function of a protein folding machine: the eukaryotic cytosolic chaperonin CCT. FEBS Lett 529: 11-16 (Pubitemid 35283904)
39. Virshup DM, Shenolikar S (2009) From promiscuity to precision: protein phosphatases get a makeover. Mol Cell 33: 537-545
40. Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M (2009) Quantitative interaction proteomics using mass spectrometry. Nat Methods 6: 203-205
41. Yeung K, Fraley C, Murua A, Raftery A, Ruzzo W (2001) Model-based clustering and data transformation for gene expression data. Bioinformatics 17: 977-987 (Pubitemid 32998635)
42. Zhang B, Park BH, Karpinets T, Samatova NF (2008) From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics 24: 979-986
43. Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L,Washburn MP (2006) Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 5: 2339-2347