Protein complex analysis: From raw protein lists to protein interaction networks

Mass Spectrometry Reviews

Volumn 36, Issue 5, 2017, Pages 600-614

  Meysman, Pieter ^a,b   Titeca, Kevin ^c,d   Eyckerman, Sven ^c,d   Tavernier, Jan ^c,d   Goethals, Bart ^a   Martens, Lennart ^c,d   Valkenborg, Dirk ^a,e,f   Laukens, Kris ^a,b  

^a UNIVERSITY OF ANTWERP   (Belgium)

^b ANTWERP UNIVERSITY HOSPITAL   (Belgium)

^c DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^d GHENT UNIVERSITY   (Belgium)

^e FLEMISH INSTITUTE FOR TECHNOLOGICAL RESEARCH VITO   (Belgium)

^f HASSELT UNIVERSITY   (Belgium)

Author keywords

bioinformatics; co complex purification; protein protein interaction networks

Indexed keywords

BIOINFORMATICS; COBALT COMPOUNDS; COMPUTATIONAL METHODS; MASS SPECTROMETRY; PROTEINS; PURIFICATION;

AFFINITY PURIFICATION; CO COMPLEXES; EXPERIMENTAL TECHNIQUES; KNOWLEDGE EXTRACTION; PROTEIN COMPLEXES; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTION NETWORKS; UNSOLVED PROBLEMS;

COMPLEX NETWORKS;

MULTIPROTEIN COMPLEX; PROTEIN;

BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; METABOLISM; PROCEDURES; PROTEIN ANALYSIS; PROTEIN DATABASE; QUALITY CONTROL; REPRODUCIBILITY; STANDARDS; WORKFLOW;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MULTIPROTEIN COMPLEXES; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEINS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; WORKFLOW;

EID: 84952837016     PISSN: 02777037     EISSN: 10982787     Source Type: Journal    
DOI: 10.1002/mas.21485     Document Type: Review

References (186)

1. Aloy P, Russell RB. 2003. InterPreTS: Protein Interaction Prediction through Tertiary Structure. Bioinformatics 19:161–162.
2. Altenhoff AM, Dessimoz C. 2012. Inferring orthology and paralogy. Methods Mol Biol 855:259–279.
3. Altenhoff AM, Škunca N, Glover N, Train C-M, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. 2015. The OMA orthology database in 2015: Function predictions, better plant support, synteny view and other improvements. Nucl Acids Res 43:D240–D249.
4. Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang H, Hirai A, Tsuzuki K, Nakamura S, Altaf-ul-amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H. 2006. Large-scale identification of protein - protein interaction of Escherichia coli K-12. Genome Res 16:686–691.
5. Armean IM, Lilley KS, Trotter MWB. 2012. Popular computational methods to assess multi-protein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Mol Cell Proteomics 12:1–13.
6. Asara JM, Christofk HR, Freimark LM, Cantley LC. 2008. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics 8:994–999.
7. 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.
8. Asthana S, King OD, Gibbons FD, Roth FP. 2004. Predicting protein complex membership using probabilistic network reliability. Genome Res 14:1170–1175.
9. Bader GG, Hogue CC. 2003. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2.
10. Barabási A. 1999. Emergence of scaling in random networks. Science 286:509–512.
11. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. 2013. NCBI GEO: Archive for functional genomics data sets-update. Nucl Acids Res 41:D991–D995.
12. Ben-Hur A, Noble WS. 2005. Kernel methods for predicting protein-protein interactions. Bioinformatics 21:i38–i46.
13. Bittremieux W, Kelchtermans P, Valkenborg D, Martens L, Laukens K. 2014. JqcML: An open-source java API for mass spectrometry quality control data in the qcML format. J Proteome Res 13:3484–3487.
14. Bittremieux W, Willems H, Kelchtermans P, Martens L, Laukens K, Valkenborg D. 2015. IMonDB: Mass spectrometry quality control through instrument monitoring. J Proteome Res 14:2360–2366.
15. Bock JR, Gough DA. 2001. Predicting protein-protein interactions from primary structure. Bioinformatics 17:455–460.
16. Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, Yu H, Sahalie JM, Murray RR, Roncari L, de Smet A-S, Venkatesan K, Rual J-F, 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.
17. Brown KR, Otasek D, Ali M, McGuffin MJ, Xie W, Devani B, Toch IL, van Jurisica I. 2009. NAViGaTOR: Network analysis, visualization and graphing Toronto. Bioinformatics 25:3327–3329.
18. Butland G, Peregrín-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A, Imaizumi-Anraku H, Webb J, Takeda N, Kojima T, Charpentier M, Oldroyd G, Perry J, Soll J, Miwa H, Kru J, Umehara Y, Kouchi H, Research C, Murakami Y, Mulder L, Vickers K, Pike J, Downie JA, Wang T, Sato S, Asamizu E, Tabata S, Yoshikawa M, Murooka Y, Wu G-J, Kawaguchi M, Kawasaki S, Parniske M, Hayashi M. 2005. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433:527–531.
19. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD. 2012. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucl Acids Res 40:D742–D753.
20. Chen X-W, Liu M. 2005. Prediction of protein-protein interactions using random decision forest framework. Bioinformatics 21:4394–4400.
21. Chen P-Y, Deane CM, Reinert G. 2008. Predicting and validating protein interactions using network structure. PLoS Comput Biol 4:e1000118.
22. Choi H, Kim S, Gingras A-C, Nesvizhskii AI. 2010. Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data. Mol Syst Biol 6:385.
23. Choi H, Glatter T, Gstaiger M, Nesvizhskii AI. 2012. SAINT-MS1: Protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments. J Proteome Res 11:2619–2624.
24. Ciriello G, Guerra C. 2008. A review on models and algorithms for motif discovery in protein-protein interaction networks. Brief Funct Genomics Proteomic 7:147–156.
25. Cloutier P, Al-Khoury R, Lavallée-Adam M, Faubert D, Jiang H, Poitras C, Bouchard A, Forget D, Blanchette M, Coulombe B. 2009. High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. Methods 48:381–386.
26. Collins MO, Choudhary JS. 2008. Mapping multiprotein complexes by affinity purification and mass spectrometry. Curr Opin Biotechnol 19:324–330.
27. Collins SR, Kemmeren P, Zhao X-C, Greenblatt JF, Spencer F, Holstege FCP, Weissman JS, Krogan NJ. 2007. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cel Proteomics 6:439–450.
28. Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R. 2013. Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system. Nat Methods 10:1246–1253.
29. Comeau SR, Gatchell DW, Vajda S, Camacho CJ. 2003. ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20:45–50.
30. Couzens AL, Knight JDR, Kean MJ, Teo G, Weiss A, Dunham WH, Lin Z-Y, Bagshaw RD, Sicheri F, Pawson T, Wrana JL, Choi H, Gingras A-C. 2013. Protein interaction network of the mammalian hippo pathway reveals mechanisms of kinase-phosphatase interactions. Sci Signaling 6:15.
31. Cox J, Mann M. 2008. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372.
32. Dandekar T. 1998. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem Sci 23:324–328.
33. Dang TH, Van Leemput K, Verschoren A, Laukens K. 2008. Prediction of kinase-specific phosphorylation sites using conditional random fields. Bioinformatics 24:2857–2864.
34. Davis D, Yaveroğlu ÖN, Malod-Dognin N, Stojmirovic A, Pržulj N. 2015. Topology-function conservation in protein-protein interaction networks. Bioinformatics 31:1632–1639.
35. Deane CM, Salwiński Ł, Xenarios I, Eisenberg D. 2002. Protein interactions: Two methods for assessment of the reliability of high throughput observations. Mol Cel Proteomics 1:349–356.
36. Dunham WH, Mullin M, Gingras AC. 2012. Affinity-purification coupled to mass spectrometry: Basic principles and strategies. Proteomics 12:1576–1590.
37. Edwards AM, Kus B, Jansen R, Greenbaum D, Greenblatt J, Gerstein M. 2002. Bridging structural biology and genomics: Assessing protein interaction data with known complexes. Trends Genet 18:529–536.
38. Eng JK, McCormack AL, Yates JR. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976–989.
39. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86–90.
40. Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucl Acids Res 30:1575–1584.
41. Eren K, Deveci M, Küçüktunç O, Catalyürek UV. 2012. A comparative analysis of biclustering algorithms for gene expression data. Brief Bioinform 14:279–292.
42. Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert J-P, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams S-L, Moran MF, Morin GB, Topaloglou T, Figeys D. 2007. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 3:89.
43. Eyckerman S, Verhee A, der Heyden JV, Lemmens I, Ostade XV, Vandekerckhove J, Tavernier J. 2001. Design and application of a cytokine-receptor-based interaction trap. Nat Cell Biol 3:1114–1119.
44. Fabre B, Lambour T, Bouyssié D, Menneteau T, Monsarrat B, Burlet-Schiltz O, Bousquet-Dubouch M-P. 2014. Comparison of label-free quantification methods for the determination of protein complexes subunits stoichiometry. EuPA Open Proteomics 4:82–86.
45. Fermin D, Avtonomov D, Choi H, Nesvizhskii AI. 2015. LuciPHOr2: Site localization of generic post-translational modifications from tandem mass spectrometry data. Bioinformatics 31:1141–1143.
46. Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MDR, Zografos L, Armstrong JD, Choudhary JS, Grant SGN. 2009. Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins. Mol Syst Biol 5:269.
47. Fernández-Recio J, Sternberg MJE. 2010. The 4th meeting on the critical assessment of predicted interaction (CAPRI) held at the mare nostrum, Barcelona. Proteins: Struct Funct Bioinf 78:3065–3066.
48. Fieulaine S, Morera S, Poncet S, Mijakovic I, Galinier A, Janin J, Deutscher J, Nessler S. 2002. X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr. Proc Natl Acad Sci USA 99:13437–13441.
49. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJP, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Zerbino DR, Searle SMJ. 2014. Ensembl 2014. Nucl Acids Res 42:D749–D755.
50. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. 2013. STRING v9.1: Protein-protein interaction networks, with increased coverage and integration. Nucl Acids Res 41:D808–D815.
51. Gaasterland T, Ragan MA. 1998. Microbial genescapes: Phyletic and functional patterns of ORF distribution among Prokaryotes. Microb Comp Genomics 3:199–217.
52. Gabaldón T, Koonin EV. 2013. Functional and evolutionary implications of gene orthology. Nat Rev Genet 14:360–366.
53. Galperin MY, Makarova KS, Wolf YI, Koonin EV. 2015. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucl Acids Res 43:D261–D269.
54. Gavin A-C, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier M-A, Hoffman V, Hoefert C, Klein K, Hudak M, Michon A-M, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G. 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631–636.
55. Gavin A-C, Maeda K, Kühner S. 2011. Recent advances in charting protein-protein interaction: Mass spectrometry-based approaches. Curr Opin Biotechnol 22:42–49.
56. Ge H, Liu Z, Church GM, Vidal M. 2001. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29:482–486.
57. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs M a, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin A-C. 2010. Visualization of omics data for systems biology. Nat Methods 7:S56.
58. Ghazizadeh S, Chawathe SS. 2002. SEuS: Structure Extraction Using Summaries. Proceedings of the 5th International Conference on Discovery Science 71–85.
59. Gibson TJ, Seiler M, Veitia RA. 2013. The transience of transient overexpression. Nat Methods 10:715–721.
60. Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. 2012. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis. Mol Cellular Proteomics 11:O111.016717.
61. Gingras A-C, Gstaiger M, Raught B, Aebersold R. 2007. Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 8:645–654.
62. 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.
63. Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. 2000. Co-evolution of proteins with their interaction partners. J Mol Biol 299:283–293.
64. Goldberg DS, Roth FP. 2003. Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci USA 100:4372–4376.
65. Goldovsky L, Cases I, Enright AJ, Ouzounis CA. 2005. BioLayout(Java): Versatile network visualisation of structural and functional relationships. Appl Bioinformatics 4:71–74.
66. Gomez SM, Noble WS, Rzhetsky A. 2003. Learning to predict protein-protein interactions from protein sequences. Bioinformatics 19:1875–1881.
67. Grossmann A, Benlasfer N, Birth P, Hegele A, Wachsmuth F, Apelt L, Stelzl U. 2015. Phospho-tyrosine dependent protein-protein interaction network. Mol Syst Biol 11:794.
68. Guo Y, Yu L, Wen Z, Li M. 2008. Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucl Acids Res 36:3025–3030.
69. Guo Y, Li M, Pu X, Li G, Guang X, Xiong W, Li J. 2010. PRED_PPI: A server for predicting protein-protein interactions based on sequence data with probability assignment. BMC Res Notes 3:145.
70. Guruharsha KG, Rual J-F, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, McKillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, VijayRaghavan K, Gygi SP, Celniker SE, Obar RA, Artavanis-Tsakonas S. 2011. A protein complex network of Drosophila melanogaster. Cell 147:690–703.
71. 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.
72. Havugimana P, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig S a, Hu P, Wan C, Vlasblom J, Dar V-NUN, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ERM, Paccanaro A, Marcotte EM, Emili A. 2012. A census of human soluble protein complexes. Cell 150:1068–1081.
73. Ho Y, Gruhler A, Heilbut a, Bader G, Moore L, Adams S, 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 A, Sassi H, Nielsen PA, Rasmussen K, Andersen J, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen B, Matthiesen J, Hendrickson R, Gleeson F, Pawson T, Moran M, Durocher D, Mann M, Hogue C, Figeys D, Tyers M. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180–183.
74. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P. 2008. Genevestigator v3: A reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 2008:420747.
75. Hu Z, Hung J-H, Wang Y, Chang Y-C, Huang C-L, Huyck M, DeLisi C. 2009. VisANT 3.5: Multi-scale network visualization, analysis and inference based on the gene ontology. Nucl Acids Res 37:W115–W121.
76. Huang S-Y. 2014. Search strategies and evaluation in protein-protein docking: Principles, advances and challenges. Drug Discov Today 19:1081–1096.
77. Hubner NC, Mann M. 2011. Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC). Methods 53:453–459.
78. Hue M, Riffle M, Vert J-P, Noble WS. 2010. Large-scale prediction of protein-protein interactions from structures. BMC Bioinformatics 11:144.
79. Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, Erickson BK, Wühr M, Chick J, Zhai B, Kolippakkam D, Mintseris J, Obar RA, Harris T, Artavanis-Tsakonas S, Sowa ME, De Camilli P, Paulo JA, Harper JW, Gygi SP. 2015. The BioPlex network: A systematic exploration of the human interactome. Cell 162:425–440.
80. Huynen M. 2000. Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res 10:1204–1210.
81. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby D a, Alber T, Cagney G, Bushman FD, Young J a, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. 2011. Global landscape of HIV-human protein complexes. Nature 481:5–10.
82. Janin J, Séraphin B. 2003. Genome-wide studies of protein-protein interaction. Curr Opin Struct Biol 13:383–388.
83. Jansen R, Greenbaum D, Gerstein M. 2002. Relating whole-genome expression data with protein-protein interactions. Genome Res 12:37–46.
84. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449–453.
85. Jiang C, Coenen F, Zito M. 2012. A survey of frequent subgraph mining algorithms. Knowl Eng Rev 28:75–105.
86. Juan D, Pazos F, Valencia A. 2008. High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci USA 105:934–939.
87. Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen W-H, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin A-C. 2009. Proteome organization in a genome-reduced bacterium. Science 326:1235–1240.
88. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. 2012. KEGG for integration and interpretation of large-scale molecular data sets. Nucl Acids Res 40:D109–D114.
89. Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H. 2012. The IntAct molecular interaction database in 2012. Nucl Acids Res 40:D841–D846.
90. Kotlyar M, Pastrello C, Pivetta F, Lo Sardo A, Cumbaa C, Li H, Naranian T, Niu Y, Ding Z, Vafaee F, Broackes-Carter F, Petschnigg J, Mills GB, Jurisicova A, Stagljar I, Maestro R, Jurisica I. 2015. In silico prediction of physical protein interactions and characterization of interactome orphans. Nat Methods 12:79–84.
91. Kouranov A, Xie L, de la Cruz J, Chen L, Westbrook J, Bourne PE, Berman HM. 2006. The RCSB PDB information portal for structural genomics. Nucl Acids Res 34:D302–D305.
92. Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S. 2013. How good is automated protein docking?. Proteins 81:2159–2166.
93. Kristensen DM, Wolf YI, Mushegian AR, Koonin EV. 2011. Computational methods for Gene Orthology inference. Brief Bioinform 12:379–391.
94. Kristensen AR, Gsponer J, Foster LJ. 2012. A high-throughput approach for measuring temporal changes in the interactome. Nat Methods 9:907–909.
95. Krumsiek J, Friedel CC, Zimmer R. 2008. ProCope-protein complex prediction and evaluation. Bioinformatics 24:2115–2116.
96. Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A. 2012. RNA-Seq Atlas-a reference database for gene expression profiling in normal tissue by next-generation sequencing. Bioinformatics 28:1184–1185.
97. Lambert J-P, Ivosev G, Couzens AL, Larsen B, Taipale M, Lin Z-Y, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras A-C. 2013. Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nat Methods 10:1239–1245.
98. Laukens K, Naulaerts S, Berghe Vanden W. 2014. Bioinformatics approaches for the functional interpretation of protein lists: From ontology term enrichment to network analysis. Proteomics 15:981–996.
99. Lavallée-Adam M, Cloutier P, Coulombe B, Blanchette M. 2011. Modeling contaminants in AP-MS/MS experiments. J Proteome Res 10:886–895.
100. Lensink MF, Wodak SJ. 2013. Docking, scoring, and affinity prediction in CAPRI. Proteins 81:2082–2095.
101. Li L, Stoeckert CJ, Roos DS. 2003. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189.
102. Lievens S, Lemmens I, Tavernier J. 2009. Mammalian two-hybrids come of age. Trends Biochem Sci 34:579–588.
103. Lin X, Chen X. 2013. Heterogeneous data integration by tree-augmented naïve Bayes for protein-protein interactions prediction. Proteomics 13:261–268.
104. Malovannaya A, Lanz RB, Jung SY, Bulynko Y, Le NT, Chan DW, Ding C, Shi Y, Yucer N, Krenciute G, Kim BJ, Li C, Chen R, Li W, Wang Y, O'Malley BW, Qin J. 2011. Analysis of the human endogenous coregulator complexome. Cell 145:787–799.
105. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. 1999. A combined algorithm for genome-wide prediction of protein function. Nature 402:83–86.
106. Martin S, Roe D, Faulon J-L. 2005. Predicting protein-protein interactions using signature products. Bioinformatics 21:218–226.
107. 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.
108. Mellacheruvu D, Wright Z, Couzens AL, Lambert J-P, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin Z-Y, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJR, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras A-C, Nesvizhskii AI. 2013. The CRAPome: A contaminant repository for affinity purification-mass spectrometry data. Nat Methods 10:730–736.
109. Melquiond ASJ, Karaca E, Kastritis PL, Bonvin AMJJ. 2012. Next challenges in protein-protein docking: From proteome to interactome and beyond. Wiley Interdiscip Rev Comput Mol Sci 2:642–651.
110. Meysman P, Sonego P, Bianco L, Fu Q, Ledezma-Tejeida D, Gama-Castro S, Liebens V, Michiels J, Laukens K, Marchal K, Collado-Vides J, Engelen K, Qiang F. 2014. COLOMBOS v2.0: An ever expanding collection of bacterial expression compendia. Nucleic Acids Res 42:D649–D653.
111. Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H. 2008. InteroPORC: Automated inference of highly conserved protein interaction networks. Bioinformatics 24:1625–1631.
112. Milenković T, Przulj N. 2008. Uncovering biological network function via graphlet degree signatures. Cancer Inform 6:257–273.
113. Moreira IS, Fernandes PA, Ramos MJ. 2010. Protein-protein docking dealing with the unknown. J Comput Chem 31:317–342.
114. Morell M, Ventura S, Avilés FX. 2009. Protein complementation assays: Approaches for the in vivo analysis of protein interactions. FEBS Lett 583:1684–1691.
115. Najafabadi HS, Salavati R. 2008. Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol 9:R87.
116. Naulaerts S, Meysman P, Bittremieux W, Vu TN, Vanden Berghe W, Goethals B, Laukens K. 2015. A primer to frequent itemset mining for bioinformatics. Brief Bioinform 16:216–231.
117. Nesvizhskii AI. 2012. Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 12:1639–1655.
118. Newman M, Girvan M. 2004. Finding and evaluating community structure in networks. Phys Rev E 69:026113.
119. Nogales E, Wolf SG, Downing KH. 1998. Structure of the alpha beta tubulin dimer by electron crystallography. Nature 391:199–203.
120. Oeffinger M. 2012. Two steps forward-one step back: Advances in affinity purification mass spectrometry of macromolecular complexes. Proteomics 12:1591–1608.
121. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing K a, Ahn NG. 2005. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4:1487–1502.
122. Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, Frings O, Sonnhammer ELL. 2010. InParanoid 7: New algorithms and tools for eukaryotic orthology analysis. Nucl Acids Res 38:D196–D203.
123. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N. 1999. Use of contiguity on the chromosome to predict functional coupling. In Silico Biol 1:93–108.
124. Płociński P, Laubitz D, Cysewski D, Stoduś K, Kowalska K, Dziembowski A. 2014. Identification of protein partners in mycobacteria using a single-step affinity purification method. PLoS ONE 9:e91380.
125. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stümpflen V, Mewes HW, Ruepp A, Frishman D. 2005. The MIPS mammalian protein-protein interaction database. Bioinformatics 21:832–834.
126. Pavlopoulos G, Wegener A, Schneider R. 2008. A survey of visualization tools for biological network analysis. BioData Mining 1:12.
127. Pazos F, Valencia A. 2001. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 14:609–614.
128. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. 1999. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc Natl Acad Sci 96:4285–4288.
129. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551–3567.
130. Pichler P, Mazanek M, Dusberger F, Weilnböck L, Huber CG, Stingl C, Luider TM, Straube WL, Köcher T, Mechtler K. 2012. SIMPATIQCO: A server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments. J Proteome Res 11:5540–5547.
131. Pierce BG, Wiehe K, Hwang H, Kim B-H, Vreven T, Weng Z. 2014. ZDOCK server: Interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics 30:1771–1773.
132. Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A. 2006. PIPE: A protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics 7:365.
133. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. 2014. EggNOG v4.0: Nested orthology inference across 3686 organisms. Nucl Acids Res 42:D231–D239.
134. Przulj N, Corneil DG, Jurisica I. 2004. Modeling interactome: Scale-free or geometric?. Bioinformatics 20:3508–3515.
135. Pu S, Vlasblom J, Turinsky A, Marcon E, Phanse S, Trimble SS, Olsen J, Greenblatt J, Emili A, Wodak SJ. 2015. Extracting high confidence protein interactions from affinity purification data: At the crossroads. J Proteomics 118:63–80.
136. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD. 2012. The Pfam protein families database. Nucl Acids Res 40:D290–D301.
137. Razick S, Magklaras G, Donaldson IM. 2008. IRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics 9:405.
138. Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM. 2005. Probabilistic model of the human protein-protein interaction network. Nat Biotechnol 23:951–959.
139. Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis A-R, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere J-C, Vega K, Walsh J, Cusick ME, Xia Y, Barabási A-L, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M. 2014. A proteome-scale map of the human interactome network. Cell 159:1212–1226.
140. Roux KJ, Kim DI, Raida M, Burke B. 2012. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol 196:801–810.
141. Rudnick PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham A-JL, Jaffe JD, Kinsinger CR, Mesri M, Neubert TA, Schilling B, Tabb DL, Tegeler TJ, Vega-Montoto L, Variyath AM, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Carr SA, Fisher SJ, Gibson BW, Paulovich AG, Regnier FE, Rodriguez H, Spiegelman C, Tempst P, Liebler DC, Stein SE. 2010. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics 9:225–241.
142. Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. 2004. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 14:313–324.
143. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U. 2013. ArrayExpress update–trends in database growth and links to data analysis tools. Nucl Acids Res 41:D987–D990.
144. 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.
145. Selbach M, Mann M. 2006. Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat Methods 3:981–983.
146. 70 senses sequence and conformation of the promoter spacer region. Nucl Acids Res 39:5109–5118.
147. Skarra DV, Goudreault M, Choi H, Mullin M, Nesvizhskii AI, Gingras AC, Honkanen RE. 2011. Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5. Proteomics 11:1508–1516.
148. Smialowski P, Pagel P, Wong P, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Rattei T, Frishman D, Ruepp A. 2009. The Negatome database: A reference set of non-interacting protein pairs. Nucl Acids Res 38:540–544.
149. Smith GR, Sternberg MJE. 2002. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12:28–35.
150. Smits AH, Jansen PWTC, Poser I, Hyman AA, Vermeulen M. 2013. Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics. Nucl Acids Res 41:1–8.
151. Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T. 2011. Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 27:431–432.
152. Sowa ME, Bennett EJ, Gygi SP, Harper JW. 2009. Defining the human deubiquitinating enzyme interaction landscape. Cell 138:389–403.
153. Sprinzak E, Margalit H. 2001. Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 311:681–692.
154. Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O. 2008. OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 9:163.
155. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062–6067.
156. Suderman M, Hallett M. 2007. Tools for visually exploring biological networks. Bioinformatics 23:2651–2659.
157. Suter B, Kittanakom S, Stagljar I. 2008. Two-hybrid technologies in proteomics research. Curr Opin Biotechnol 19:316–323.
158. Tamames J, Casari G, Ouzounis C, Valencia A. 1997. Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol 44:66–73.
159. Tarassov K, Messier V, Landry CR, Radinovic S, Serna Molina MM, Shames I, Malitskaya Y, Vogel J, Bussey H, Michnick SW. 2008. An in vivo map of the yeast protein interactome. Science 320:1465–1470.
160. Teo G, Liu G, Zhang J, Nesvizhskii AI, Gingras AC, Choi H. 2014. SAINTexpress: Improvements and additional features in significance analysis of INTeractome software. J Proteomics 100:37–43.
161. Terrak M, Kerff F, Langsetmo K, Tao T, Dominguez R. 2004. Structural basis of protein phosphatase 1 regulation. Nature 429:780–784.
162. Titeca K, Meysman P, Gevaert K, Tavernier J, Laukens K, Martens L, Eyckerman S. 2015. SFINX: Straightforward filtering index for affinity purification-mass spectrometry data analysis. J Proteome Res. doi: 10.1021/acs.jproteome.5b00666.
163. Torchala M, Moal IH, Chaleil RAG, Fernandez-Recio J, Bates PA. 2013. SwarmDock: A server for flexible protein-protein docking. Bioinformatics 29:807–809.
164. Tsou C-C, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras A-C, Nesvizhskii AI. 2015. DIA-Umpire: Comprehensive computational framework for data-independent acquisition proteomics. Nat Methods 12:258–264.
165. Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Björling L, Ponten F. 2010. Towards a knowledge-based Human Protein Atlas. Nat Biotechnol 28:1248–1250.
166. van Dijk M, van Dijk ADJ, Hsu V, Boelens R, Bonvin AMJJ. 2006. Information-driven protein-DNA docking using HADDOCK: It is a matter of flexibility. Nucl Acids Res 34:3317–3325.
167. Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdael G, Verkest A, Neirynck S, Buffel Y, De Bodt S, Maere S, Laukens K, Pharazyn A, Ferreira PCG, Eloy N, Renne C, Meyer C, Faure J-D, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inzé D, Witters E, De Jaeger G. 2010. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol 6:397.
168. van Nuland R, Smits AH, Pallaki P, Jansen PWTC, Vermeulen M, Timmers HTM. 2013. Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes. Mol Cell Biol 33:2067–2077.
169. Varjosalo M, Sacco R, Stukalov A, van Drogen A, Planyavsky M, Hauri S, Aebersold R, Bennett KL, Colinge J, Gstaiger M, Superti-Furga G. 2013. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nat Methods 10:307–314.
170. Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H. 2015. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol 33:22–24.
171. Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HWP, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJR, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L. 2014. QcML: An exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics 13:1905–1913.
172. Walzthoeni T, Leitner A, Stengel F, Aebersold R. 2013. Mass spectrometry supported determination of protein complex structure. Curr Opin Struct Biol 23:252–260.
173. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476.
174. Wass MN, Fuentes G, Pons C, Pazos F, Valencia A. 2011. Towards the prediction of protein interaction partners using physical docking. Mol Syst Biol 7:469.
175. Wingender E, Dietze P, Karas H, Knüppel R. 1996. TRANSFAC: A database on transcription factors and their DNA binding sites. Nucl Acids Res 24:238–241.
176. Wuchty S. 2006. Topology and weights in a protein domain interaction network-a novel way to predict protein interactions. BMC Genomics 7:122.
177. Xia J-F, Han K, Huang D-S. 2010. Sequence-based prediction of protein-protein interactions by means of rotation forest and autocorrelation descriptor. Protein Pept Lett 17:137–145.
178. Xie Z, Kwoh CK, Li XL, Wu M. 2011. Construction of co-complex score matrix for protein complex prediction from AP-MS data. Bioinformatics 27.
179. Xue Y, Ren J, Gao X, Jin C, Wen L, Yao X. 2008. GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics 7:1598–1608.
180. Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H. 2004. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci USA 101:5934–5939.
181. Yu H, Paccanaro A, Trifonov V, Gerstein M. 2006. Predicting interactions in protein networks by completing defective cliques. Bioinformatics 22:823–829.
182. Yu J, Pacifico S, Liu G, Finley RL. 2008. DroID: The Drosophila interactions database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 9:461.
183. Yu C-Y, Chou L-C, Chang DT-H. 2010. Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. BMC Bioinformatics 11:167.
184. 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.
185. Zhang SJ, Hagenbuchner M, Scarselli F, Tsoi AC. 2010. Supervised encoding of graph-of-graphs for classification and regression problems. Lect Notes Comput Sci 6203:449–461.
186. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. 2012. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490:556–560.