Large-scale mapping of human protein-protein interactions by mass spectrometry

Molecular Systems Biology

Volumn 3, Issue , 2007, Pages

  Ewing, Rob M ^a,b   Chu, Peter ^a,e   Elisma, Fred ^c   Li, Hongyan ^a,f   Taylor, Paul ^a,g   Climie, Shane ^a,h   McBroom Cerajewski, Linda ^a,d   Robinson, Mark D ^a,i   O'Connor, Liam ^a,j   Li, Michael ^a,k   Taylor, Rod ^a   Dharsee, Moyez ^a,b   Ho, Yuen ^a,d   Heilbut, Adrian ^a,l   Moore, Lynda ^a,m   Zhang, Shudong ^a   Ornatsky, Olga ^a,n   Bukhman, Yury V ^a,o   Ethier, Martin ^c   Sheng, Yinglun ^c   Vasilescu, Julian ^c   Abu Farha, Mohamed ^c   Lambert, Jean Philippe ^c   Duewel, Henry S ^a,p   Stewart, Ian I ^a,b   Kuehl, Bonnie ^a,q   Hogue, Kelly ^a,g   Colwill, Karen ^a,r   Gladwish, Katharine ^a   Muskat, Brenda ^a,s   Kinach, Robert ^a,n   Adams, Sally Lin ^a,g   Moran, Michael F ^a,g   Morin, Gregg B ^a,m   Topaloglou, Thodoros ^a,d   Figeys, Daniel ^a,c   more..

^a Transition Therapeutics   (Canada)

^b Infochromics   (Canada)

^c UNIVERSITY OF OTTAWA   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

^e MCMASTER UNIVERSITY   (Canada)

^f YORK UNIVERSITY   (Canada)

^g HOSPITAL FOR SICK CHILDREN   (Canada)

^h Popper and Company LLC   (United States)

ⁱ WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^j NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^k Platform Computing Inc   (Canada)

^l Department of Preclinical Development and Formulations   (United States)

^m CANADA'S MICHAEL SMITH GENOME SCIENCES CENTRE   (Canada)

ⁿ UNIVERSITY OF TORONTO   (Canada)

^o PRINCESS MARGARET HOSPITAL   (Canada)

^p Sigma Aldrich Co   (United States)

^q Scientific Insights Consulting Group Inc   (Canada)

^r MOUNT SINAI HOSPITAL   (Canada)

^s MDS Inc   (Canada)

more..

Author keywords

Human interactome; IP HTMS; Protein protein interaction

Indexed keywords

ARTICLE; COMPARATIVE STUDY; CONFIDENCE INTERVAL; DATA ANALYSIS; EMBRYO; GENE EXPRESSION; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; MASS SPECTROMETRY; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; PARALOGY; PEPTIDE ANALYSIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; SCORING SYSTEM; VALIDATION PROCESS; ELECTROSPRAY MASS SPECTROMETRY; METABOLISM; METHODOLOGY; PROTEIN BINDING;

PROTEIN;

HUMANS; IMMUNOPRECIPITATION; PROTEIN BINDING; PROTEINS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 33947219266     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100134     Document Type: Article

References (53)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29
2. Bader GD, Hogue CW (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 20: 991-997
3. Barrios-Rodiles M, Brown KR, Ozdamar B, Bose R, Liu Z, Donovan RS, Shinjo F, Liu Y, Dembowy J, Taylor IW, Luga V, Przulj N, Robinson M, Suzuki H, Hayashizaki Y, Jurisica I, Wrana JL (2005) High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307: 1621-1625
4. Belham C, Roig J, Caldwell JA, Aoyama Y, Kemp BE, Comb M, Avruch J (2003) A mitotic cascade of NIMA family kinases. Nercc1/Nek9 activates the Nek6 and Nek7 kinases. J Biol Chem 278: 34897-34909
5. Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, Croughton K, Cruciat C, Eberhard D, Gagneur J, Ghidelli S, Hopf C, Huhse B, Mangano R, Michon AM, Schirle M, Schlegl J, Schwab M, Stein MA, Bauer A, Casari G, Drewes G, Gavin AC, Jackson DB, Joberty G, Neubauer G, Rick J, Kuster B, Superti-Furga G (2004) A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 6: 97-105
6. Bowers AJ, Boylan JF (2004) Nek8, a NIMA family kinase member, is overexpressed in primary human breast tumors. Gene 328: 135-142
7. Bradshaw RA, Burlingame AL, Carr S, Aebersold R (2006) Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics 5: 787-788
8. Chien CT, Bartel PL, Sternglanz R, Fields S (1991) The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. Proc Natl Acad Sci USA 88: 9578-9582
9. De Souza CP, Horn KP, Masker K, Osmani SA (2003) The SONB(NUP98) nucleoporin interacts with the NIMA kinase in Aspergillus nidulans. Genetics 165: 1071-1081
10. De Souza CP, Osmani AH, Hashmi SB, Osmani SA (2004) Partial nuclear pore complex disassembly during closed mitosis in Aspergillus nidulans. Curr Biol 14: 1973-1984
11. Deane CM, Salwinski L, Xenarios I, Eisenberg D (2002) Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 1: 349-356
12. Eichenmuller B, Everley P, Palange J, Lepley D, Suprenant KA (2002) The human EMAP-like protein-70 (ELP70) is a microtubule destabilizer that localizes to the mitotic apparatus. J Biol Chem 277: 1301-1309
13. Figeys D, McBroom LD, Moran MF (2001) Mass spectrometry for the study of protein-protein interactions. Methods 24: 230-239
14. Fletcher CM, Pestova TV, Hellen CU, Wagner G (1999) Structure and interactions of the translation initiation factor eIF1. EMBO J 18: 2631-2637
15. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147
16. Ge H, Liu Z, Church GM, Vidal M (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29: 482-486
17. Gloeckner CJ, Mayerhofer PU, Landgraf P, Muntau AC, Holzinger A, Gerber JK, Kammerer S, Adamski J, Roscher AA (2000) Human adrenoleukodystrophy protein and related peroxisomal ABC transporters interact with the peroxisomal assembly protein PEX19p. Biochem Biophys Res Commun 271: 144-150
18. Haghighat A, Mader S, Pause A, Sonenberg N (1995) Repression of cap-dependent translation by 4E-binding protein 1: competition with p220 for binding to eukaryotic initiation factor-4E. EMBO J 14: 5701-5709
19. Hahn A, Rahnenfuhrer J, Talwar P, Lengauer T (2005) Confirmation of human protein interaction data by human expression data. BMC Bioinformatics 6: 112
20. Hashimoto Y, Akita H, Hibino M, Kohri K, Nakanishi M (2002) Identification and characterization of Nek6 protein kinase, a potential human homolog of NIMA histone H3 kinase. Biochem Biophys Res Commun 293: 753-758
21. Hayward DG, Fry AM (2005) Nek2 kinase in chromosome instability and cancer. Cancer Lett 2: 2
22. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, 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 SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R (2004) The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat Biotechnol 22: 177-183
23. 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, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183
24. Jin J, Smith FD, Stark C, Wells CD, Fawcett JP, Kulkarni S, Metalnikov P, O'Donnell P, Taylor P, Taylor L, Zougman A, Woodgett JR, Langeberg LK, Scott JD, Pawson T (2004) Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization. Curr Biol 14: 1436-1450
25. Jones DH, Ley S, Aitken A (1995) Isoforms of 14-3-3 protein can form homo- and heterodimers in vivo and in vitro: implications for function as adapter proteins. FEBS Lett 368: 55-58
26. Kapp LD, Lorsch JR (2004) The molecular mechanics of eukaryotic translation. Annu Rev Biochem 73: 657-704
27. Lankat-Buttgereit B, Goke R (2003) Programmed cell death protein 4 (pdcd4): a novel target for antineoplastic therapy? Biol Cell 95: 515-519
28. Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P (2004) Co-expression analysis of human genes across many microarray data sets. Genome Res 14: 1085-1094
29. Lehner B, Fraser AG (2004) A first-draft human protein-interaction map. Genome Biol 5: R63
30. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M (2004) A map of the interactome network of the metazoan C. elegans. Science 303: 540-543
31. Liu LX, Janvier K, Berteaux-Lecellier V, Cartier N, Benarous R, Aubourg P (1999) Homo- and heterodimerization of peroxisomal ATP-binding cassette half-transporters. J Biol Chem 274: 32738-32743
32. Lu KP, Hunter T (1995) Evidence for a NIMA-like mitotic pathway in vertebrate cells. Cell 81: 413-424
33. Majumdar R, Bandyopadhyay A, Maitra U (2003) Mammalian translation initiation factor eIF1 functions with eIF1A and eIF3 in the formation of a stable 40 S preinitiation complex. J Biol Chem 278: 6580-6587
34. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M (2001) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or 'interologs'. Genome Res 11: 2120-2126
35. Moser HW (1999) Genotype-phenotype correlations in disorders of peroxisome biogenesis. Mol Genet Metab 68: 316-327
36. O'Brien KP, Remm M, Sonnhammer ELL (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 33: D476-D480
37. O'Connell MJ, Krien MJ, Hunter T (2003) Never say never. The NIMA-related protein kinases inmitotic control. Trends Cell Biol 13: 221-228
38. Pestova TV, Kolupaeva VG, Lomakin IB, Pilipenko EV, Shatsky IN, Agol VI, Hellen CU (2001) Molecular mechanisms of translation initiation in eukaryotes. Proc Natl Acad Sci USA 98: 7029-7036
39. Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM (2005) Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol 6: R40
40. Reguly T, Breitkreutz A, Boucher L, Breitkreutz B-J, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M (2006) Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol 5: 11
41. Richter JD, Sonenberg N (2005) Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature 433: 477-480
42. Richter NJ, Rogers Jr GW, Hensold JO, Merrick WC (1999) Further biochemical and kinetic characterization of human eukaryotic initiation factor 4H. J Biol Chem 274: 35415-35424
43. Roig J, Mikhailov A, Belham C, Avruch J (2002) Nercc1, a mammalian NIMA-family kinase, binds the Ran GTPase and regulates mitotic progression. Genes Dev 16: 1640-1658
44. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178
45. Steinberg SJ, Dodt G, Raymond GV, Braverman NE, Moser AB, Moser HW (2006) Peroxisome biogenesis disorders. Biochim Biophys Acta 1763: 1733-1748
46. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksoz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968
47. Sterner JM, Dew-Knight S, Musahl C, Kornbluth S, Horowitz JM (1998) Negative regulation of DNA replication by the retinoblastoma protein is mediated by its association with MCM7. Mol Cell Biol 18: 2748-2757
48. Su L, Hershberger RJ, Weissman IL (1993) LYAR, a novel nucleolar protein with zinc finger DNA-binding motifs, is involved in cell growth regulation. Genes Dev 7: 735-748
49. Unbehaun A, Borukhov SI, Hellen CU, Pestova TV (2004) Release of initiation factors from 48S complexes during ribosomal subunit joining and the link between establishment of codon-anticodon base-pairing and hydrolysis of eIF2-bound GTP. Genes Dev 18: 3078-3093
50. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403
51. Yang HS, Cho MH, Zakowicz H, Hegamyer G, Sonenberg N, Colburn NH (2004) A novel function of the MA-3 domains in transformation and translation suppressor Pdcd4 is essential for its binding to eukaryotic translation initiation factor 4A. Mol Cell Biol 24: 3894-3906
52. Yin MJ, Shao L, Voehringer D, Smeal T, Jallal B (2003) The serine/ threonine kinase Nek6 is required for cell cycle progression through mitosis. J Biol Chem 278: 52454-52460
53. Zakowicz H, Yang HS, Stark C, Wlodawer A, Laronde-Leblanc N, Colburn NH (2005) Mutational analysis of the DEAD-box RNA helicase eIF4AII characterizes its interaction with transformation suppressor Pdcd4 and eIF4GI. RNA 11: 261-274