Systematic computational prediction of protein interaction networks

Physical Biology

Volumn 8, Issue 3, 2011, Pages

  Lees, J G ^a   Heriche, J K ^b   Morilla, I ^c   Ranea, J A ^a,c   Orengo, C A ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HUMAN; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEINS;

EID: 79956188502     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/8/3/035008     Document Type: Article

References (140)

1. Kerrien S et al 2007 IntAct-open source resource for molecular interaction data Nucleic Acids Res. 35 D561-5
2. Chatr-aryamontri A, Ceol A, Palazzi L M, Nardelli G, Schneider M V, Castagnoli L and Cesareni G 2007 MINT: the Molecular INTeraction database Nucleic Acids Res. 35 D572-4
3. Xenarios I, Rice D W, Salwinski L, Baron M K, Marcotte E M and Eisenberg D 2000 DIP: the database of interacting proteins Nucleic Acids Res. 28 289-91 (Pubitemid 30047782)
4. Keshava Prasad T S et al 2009 Human protein reference database-2009 update Nucleic Acids Res. 37 D767-72
5. Ruepp A et al 2008 CORUM: the comprehensive resource of mammalian protein complexes Nucleic Acids Res. 36 D646-50
6. Stumpf M P, Thorne T, de Silva E, Stewart R, An H J, Lappe M and Wiuf C 2008 Estimating the size of the human interactome Proc. Natl Acad. Sci. USA 105 6959-64 (Pubitemid 351754512)
7. Venkatesan K et al 2009 An empirical framework for binary interactome mapping Nat. Methods 6 83-90
8. Suthram S, Sittler T and Ideker T 2005 The Plasmodium protein network diverges from those of other eukaryotes Nature 438 108-12 (Pubitemid 41599829)
9. Pellegrini M, Marcotte E M, Thompson M J, Eisenberg D and Yeates T O 1999 Assigning protein functions by comparative genome analysis: protein phylogenetic profiles Proc. Natl Acad. Sci. USA 96 4285-8 (Pubitemid 29190328)
10. Bowers P M, Cokus S J, Eisenberg D and Yeates T O 2004 Use of logic relationships to decipher protein network organization Science 306 2246-9 (Pubitemid 40024459)
11. Ranea J A, Yeats C, Grant A and Orengo C A 2007 Predicting protein function with hierarchical phylogenetic profiles: the Gene3D phylo-tuner method applied to eukaryotic genomes PLoS Comput. Biol. 3 e237
12. Barker D and Pagel M 2005 Predicting functional gene links from phylogenetic-statistical analyses of whole genomes PLoS Comput. Biol. 1 e3
13. Zhou Y, Wang R, Li L, Xia X and Sun Z 2006 Inferring functional linkages between proteins from evolutionary scenarios J. Mol. Biol. 359 1150-9 (Pubitemid 43831926)
14. Jensen L J et al 2009 STRING 8-a global view on proteins and their functional interactions in 630 organisms Nucleic Acids Res. 37 D412-6
15. Luttgen H et al 2000 Biosynthesis of terpenoids: YchB protein of Escherichia coli phosphorylates the 2-hydroxy group of 4-diphosphocytidyl-2 C-methyl-D-erythritol Proc. Natl. Acad. Sci. USA 97 1062-7 (Pubitemid 30080812)
16. Carlson B A, Xu X M, Kryukov G V, Rao M, Berry M J, Gladyshev V N and Hatfield D L 2004 Identification and characterization of phosphoseryl-tRNA[Ser] Sec kinase Proc. Natl Acad. Sci. USA 101 12848-53
17. Forterre P 2002 A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein Trends Genet. 18 236-7
18. Morett E, Korbel J O, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B and Bork P 2003 Systematic discovery of analogous enzymes in thiamin biosynthesis Nat. Biotechnol. 21 790-5 (Pubitemid 36791398)
19. Marcotte E M, Pellegrini M, Ng H L, Rice D W, Yeates T O and Eisenberg D 1999 Detecting protein function and protein-protein interactions from genome sequences Science 285 751-3
20. Zhang Z et al 2006 Genome-wide analysis of mammalian DNA segment fusion/fission J. Theor. Biol. 240 200-8
21. Reid A J, Ranea J A, Clegg A B and Orengo C A 2010 CODA: accurate detection of functional associations between proteins in eukaryotic genomes using domain fusion PLoS ONE 5 e10908
22. Gaballa A, Newton G L, Antelmann H, Parsonage D, Upton H, Rawat M, Claiborne A, Fahey R C and Helmann J D 2010 Biosynthesis and functions of bacillithiol, a major low-molecular-weight thiol in Bacilli Proc. Natl Acad. Sci. USA 107 6482-6
23. Strong M, Mallick P, Pellegrini M, Thompson M J and Eisenberg D 2003 Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach Genome Biol. 4 R59
24. Ferrer L, Dale J M and Karp P D 2010 A systematic study of genome context methods: calibration, normalization and combination BMC Bioinformatics 11 493
25. Itoh T, Takemoto K, Mori H and Gojobori T 1999 Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes Mol. Biol. Evol. 16 332-46 (Pubitemid 29119970)
26. Koonin E V, Wolf Y I and Aravind L 2001 Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach Genome Res. 11 240-52 (Pubitemid 32166533)
27. Evguenieva-Hackenberg E, Walter P, Hochleitner E, Lottspeich F and Klug G 2003 An exosome-like complex in Sulfolobus solfataricus EMBO Rep. 4 889-93 (Pubitemid 37309279)
28. Tuncbag N, Gursoy A, Guney E, Nussinov R and Keskin O 2008 Architectures and functional coverage of protein-protein interfaces J. Mol. Biol. 381 785-802
29. Tuncbag N, Kar G, Keskin O, Gursoy A and Nussinov R 2009 A survey of available tools and web servers for analysis of protein-protein interactions and interfaces Brief Bioinform 10 217-32
30. Pazos F, Helmer-Citterich M, Ausiello G and Valencia A 1997 Correlated mutations contain information about protein-protein interaction J. Mol. Biol. 271 511-23 (Pubitemid 27373087)
31. Juan D, Pazos F and Valencia A 2008 Co-evolution and co-adaptation in protein networks FEBS Lett. 582 1225-30
32. Kann M G, Shoemaker B A, Panchenko A R and Przytycka T M 2009 Correlated evolution of interacting proteins: looking behind the mirrortree J. Mol. Biol. 385 91-8
33. Pazos F and Valencia A 2001 Similarity of phylogenetic trees as indicator of protein-protein interaction Protein Eng. 14 609-14 (Pubitemid 33086280)
34. Pazos F, Ranea J A, Juan D and Sternberg M J 2005 Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome J. Mol. Biol. 352 1002-15 (Pubitemid 41267084)
35. Izarzugaza J M, Juan D, Pons C, Ranea J A, Valencia A and Pazos F 2006 TSEMA: interactive prediction of protein pairings between interacting families Nucleic Acids Res. 34 W315-9
36. Itzhaki Z, Akiva E, Altuvia Y and Margalit H 2006 Evolutionary conservation of domain-domain interactions Genome Biol. 7 R125
37. Finn R D et al 2008 The Pfam protein families database Nucleic Acids Res. 36 D281-8
38. Stein A, Panjkovich A and Aloy P 2009 3did Update: domain-domain and peptide-mediated interactions of known 3D structure Nucleic Acids Res. 37 D300-4
39. Eddy S R 2009 A new generation of homology search tools based on probabilistic inference Genome Inform 23 205-11
40. Lees J, Yeats C, Redfern O, Clegg A and Orengo C 2010 Gene3D: merging structure and function for a thousand genomes Nucleic Acids Res. 38 D296-300
41. Kim W K, Park J and Suh J K 2002 Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair Genome Inform 13 42-50
42. Chen X W and Liu M 2005 Prediction of protein-protein interactions using random decision forest framework Bioinformatics 21 4394-400 (Pubitemid 41782930)
43. Luo Q, Pagel P, Vilne B and Frishman D 2011 DIMA 3.0: domain interaction map Nucleic Acids Res. 39 D724-9
44. Bjorkholm P and Sonnhammer E L 2009 Comparative analysis and unification of domain-domain interaction networks Bioinformatics 25 3020-5
45. Schwartz A S, Yu J, Gardenour K R, Finley R L Jr and Ideker T 2009 Cost-effective strategies for completing the interactome Nat. Methods 6 55-61
46. Ben-Hur A and Noble W S 2005 Kernel methods for predicting protein-protein interactions Bioinformatics 21 (Suppl. 1) i38-46
47. Yu J, Guo M, Needham C J, Huang Y, Cai L and Westhead D R 2010 Simple sequence-based kernels do not predict protein-protein interactions Bioinformatics 26 2610-4
48. Matthews L R, Vaglio P, Reboul J, Ge H, Davis B P, Garrels J, Vincent S and Vidal M 2001 Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or 'interologs' Genome Res. 11 2120-6 (Pubitemid 33138810)
49. Mika S and Rost B 2006 Protein-protein interactions more conserved within species than across species PLoS Comput. Biol. 2 e79
50. Persico M, Ceol A, Gavrila C, Hoffmann R, Florio A and Cesareni G 2005 HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms BMC Bioinformatics 6 (Suppl. 4) S21
51. Kemmer D et al 2005 Ulysses-an application for the projection of molecular interactions across species Genome Biol. 6 R106
52. Huang T W, Lin C Y and Kao C Y 2007 Reconstruction of human protein interolog network using evolutionary conserved network BMC Bioinformatics 8 152
53. Brown K R and Jurisica I 2007 Unequal evolutionary conservation of human protein interactions in interologous networks Genome Biol. 8 R95
54. Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A and Tress M L 2009 Progress and challenges in predicting protein-protein interaction sites Brief Bioinform 10 233-46
55. Aloy P and Russell R B 2003 InterPreTS: protein interaction prediction through tertiary structure Bioinformatics 19 161-2 (Pubitemid 36150198)
56. Singh R, Park D, Xu J, Hosur R and Berger B 2010 Struct2Net: a web service to predict protein-protein interactions using a structure-based approach Nucleic Acids Res. 38 (Suppl.) W508-15
57. Hosur R, Xu J, Bienkowska J and Berger B 2011 iWRAP: an interface threading approach with application to prediction of cancer-related protein-protein interactions J. Mol. Biol. 405 1295-310
58. Zhang Q C, Petrey D, Norel R and Honig B H 2010 Protein interface conservation across structure space Proc. Natl Acad. Sci. USA 107 10896-901
59. Shoemaker B A, Zhang D, Thangudu R R, Tyagi M, Fong J H, Marchler-Bauer A, Bryant S H, Madej T and Panchenko A R 2010 Inferred biomolecular interaction server-a web server to analyze and predict protein interacting partners and binding sites Nucleic Acids Res. 38 D518-24
60. Krissinel E and Henrick K 2007 Inference of macromolecular assemblies from crystalline state J. Mol. Biol. 372 774-97 (Pubitemid 47321791)
61. Hue M, Riffle M, Vert J P and Noble W S 2010 Large-scale prediction of protein-protein interactions from structures BMC Bioinformatics 11 144
62. Grigoriev A 2001 A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae Nucleic Acids Res. 29 3513-9 (Pubitemid 32898765)
63. Bhardwaj N and Lu H 2005 Correlation between gene expression profiles and protein-protein interactions within and across genomes Bioinformatics 21 2730-8 (Pubitemid 40852321)
64. Lukk M, Kapushesky M, Nikkila J, Parkinson H, Goncalves A, Huber W, Ukkonen E and Brazma A 2010 A global map of human gene expression Nat. Biotechnol. 28 322-4
65. Adler P, Kolde R, Kull M, Tkachenko A, Peterson H, Reimand J and Vilo J 2009 Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods Genome Biol. 10 R139
66. Stuart J M, Segal E, Koller D and Kim S K 2003 A gene-coexpression network for global discovery of conserved genetic modules Science 302 249-55 (Pubitemid 37248749)
67. Hutchins J R et al 2010 Systematic analysis of human protein complexes identifies chromosome segregation proteins Science 328 593-9
68. van Steensel B, Braunschweig U, Filion G J, Chen M, van Bemmel J G and Ideker T 2010 Bayesian network analysis of targeting interactions in chromatin Genome Res. 20 190-200
69. Schaefer C F, Anthony K, Krupa S, Buchoff J, Day M, Hannay T and Buetow K H 2009 PID: the pathway interaction database Nucleic Acids Res. 37 D674-9
70. Matthews L et al 2009 Reactome knowledgebase of human biological pathways and processes Nucleic Acids Res. 37 D619-22
71. Cherry J M et al 1998 SGD: saccharomyces genome database Nucleic Acids Res. 26 73-9 (Pubitemid 28295265)
72. Amberger J, Bocchini C A, Scott A F and Hamosh A 2009 McKusick's online Mendelian inheritance in man (OMIM) Nucleic Acids Res. 37 D793-6
73. Tweedie S et al 2009 FlyBase: enhancing Drosophila Gene Ontology annotations Nucleic Acids Res. 37 D555-9
74. Blaschke C, Hoffmann R, Oliveros J C and Valencia A 2001 Extracting information automatically from biological literature Comp. Funct. Genomics 2 310-3 (Pubitemid 33064696)
75. Tikk D, Thomas P, Palaga P, Hakenberg J and Leser U 2010 A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature PLoS Comput. Biol. 6 e1000837
76. Ashburner M et al 2000 Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat. Genet. 25 25-9 (Pubitemid 30257031)
77. Pesquita C, Faria D, Falcao A O, Lord P and Couto F M 2009 Semantic similarity in biomedical ontologies PLoS Comput. Biol. 5 e1000443
78. Lord P W, Stevens R D, Brass A and Goble C A 2003 Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation Bioinformatics 19 1275-83 (Pubitemid 36850221)
79. Scott M S and Barton G J 2007 Probabilistic prediction and ranking of human protein-protein interactions BMC Bioinformatics 8 239
80. Jansen R et al 2003 A Bayesian networks approach for predicting protein-protein interactions from genomic data Science 302 449-53 (Pubitemid 37296271)
81. Bowers P M, Pellegrini M, Thompson M J, Fierro J, Yeates T O and Eisenberg D 2004 Prolinks: a database of protein functional linkages derived from coevolution Genome Biol. 5 R35
82. Sun J, Sun Y, Ding G, Liu Q, Wang C, He Y, Shi T, Li Y and Zhao Z 2007 InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes BMC Bioinformatics 8 414
83. Wilkinson D J 2007 Bayesian methods in bioinformatics and computational systems biology Brief Bioinform 8 109-16 (Pubitemid 47072261)
84. Lu L J, Xia Y, Paccanaro A, Yu H and Gerstein M 2005 Assessing the limits of genomic data integration for predicting protein networks Genome Res. 15 945-53 (Pubitemid 40994214)
85. Hwang D et al 2005 A data integration methodology for systems biology Proc. Natl Acad. Sci. USA 102 17296-301 (Pubitemid 41740860)
86. Ranea J A, Morilla I, Lees J G, Reid A J, Yeats C, Clegg A B, Sanchez-Jimenez F and Orengo C 2010 Finding the 'dark matter' in human and yeast protein network prediction and modelling PLoS Comput. Biol. 6 e1000945
87. Shawe-Taylor J and Cristianini N (ed) 2004 Kernel Methods for Pattern Analysis (Cambridge: Cambridge University Press)
88. Qiu J and Noble W S 2008 Predicting co-complexed protein pairs from heterogeneous data PLoS Comput. Biol. 4 e1000054
89. Zhou D and Schölkopf B 2004 A regularization framework for learning from graph data ICML Workshop on Statistical Relational Learning
90. Xia K, Dong D and Han J D 2006 IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model BMC Bioinformatics 7 508
91. Hwang D et al 2005 A data integration methodology for systems biology: experimental verification Proc. Natl Acad. Sci. USA 102 17302-7 (Pubitemid 41740861)
92. Qi Y, Bar-Joseph Z and Klein-Seetharaman J 2006 Evaluation of different biological data and computational classification methods for use in protein interaction prediction Proteins 63 490-500
93. Yellaboina S, Goyal K and Mande S C 2007 Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: comparison with high-throughput experimental data Genome Res. 17 527-35 (Pubitemid 46556457)
94. Qi Y, Klein-Seetharaman J and Bar-Joseph Z 2005 Random forest similarity for protein-protein interaction prediction from multiple sources Pac. Symp. Biocomput. 10 531-42
95. Mohamed T P, Carbonell J G and Ganapathiraju M K 2010 Active learning for human protein-protein interaction prediction BMC Bioinformatics 11 (Suppl. 1) S57
96. Geurts P, Irrthum A and Wehenkel L 2009 Supervised learning with decision tree-based methods in computational and systems biology Mol. Biosyst. 5 1593-605
97. Lin N, Wu B, Jansen R, Gerstein M and Zhao H 2004 Information assessment on predicting protein-protein interactions BMC Bioinformatics 5 154
98. Sprinzak E, Altuvia Y and Margalit H 2006 Characterization and prediction of protein-protein interactions within and between complexes Proc. Natl Acad. Sci. USA 103 14718-23 (Pubitemid 44527796)
99. Qi Y, Klein-Seetharaman J and Bar-Joseph Z 2007 A mixture of feature experts approach for protein-protein interaction prediction BMC Bioinformatics 8 (Suppl. 10) S6
100. Fouss F, Françoisse K, Yen L, Pirotte A and Saerens M 2006 An experimental investigation of graph kernels on a collaborative recommendation task Proc. 6th Int. Conf. on Data Mining pp 863-8
101. Kohler S, Bauer S, Horn D and Robinson P N 2008 Walking the interactome for prioritization of candidate disease genes Am. J. Human Genet. 82 949-58
102. Li Y and Patra J C 2010 Integration of multiple data sources to prioritize candidate genes using discounted rating system BMC Bioinformatics 11 (Suppl. 1) S20
103. Li Y and Patra J C 2010 Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network Bioinformatics 26 1219-24
104. Li X, Wu M, Kwoh C K and Ng S K 2010 Computational approaches for detecting protein complexes from protein interaction networks: a survey BMC Genomics 11 (Suppl. 1) S3
105. Brohee S and van Helden J 2006 Evaluation of clustering algorithms for protein-protein interaction networks BMC Bioinformatics 7 488
106. Vlasblom J and Wodak S J 2009 Markov clustering versus affinity propagation for the partitioning of protein interaction graphs BMC Bioinformatics 10 99
107. Inoue K, Li W and Kurata H 2010 Diffusion model based spectral clustering for protein-protein interaction networks PLoS ONE 5 e12623
108. Qin G and Gao L 2010 Spectral clustering for detecting protein complexes in protein-protein interaction (PPI) networks Math. Comput. Modell. 52 2066-74
109. Ding C, He X, Meraz R F and Holbrook S R 2004 A unified representation of multiprotein complex data for modeling interaction networks Proteins 57 99-108 (Pubitemid 39195886)
110. Bu D et al 2003 Topological structure analysis of the protein-protein interaction network in budding yeast Nucleic Acids Res. 31 2443-50 (Pubitemid 37442113)
111. Sen T Z, Kloczkowski A and Jernigan R L 2006 Functional clustering of yeast proteins from the protein-protein interaction network BMC Bioinformatics 7 355
112. Lima-Mendez G and van Helden J 2009 The powerful law of the power law and other myths in network biology Mol. Biosyst. 5 1482-93
113. Gomez S M and Rzhetsky A 2002 Towards the prediction of complete protein-protein interaction networks Pac. Symp. Biocomput. 7 413-24
114. Henrick K and Thornton J M 1998 PQS: a protein quaternary structure file server Trends Biochem. Sci. 23 358-61 (Pubitemid 28461869)
115. Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes H W and Stumpflen V 2006 MPact: the MIPS protein interaction resource on yeast Nucleic Acids Res. 34 D436-41
116. Hart G T, Lee I and Marcotte E R 2007 A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality BMC Bioinformatics 8 236
117. Pu S, Wong J, Turner B, Cho E and Wodak S J 2009 Up-to-date catalogues of yeast protein complexes Nucleic Acids Res. 37 825-31
118. Yu H et al 2008 High-quality binary protein interaction map of the yeast interactome network Science 322 104-10
119. Smialowski P et al 2010 The Negatome database: a reference set of non-interacting protein pairs Nucleic Acids Res. 38 D540-4
120. Browne F, Wang H, Zheng H and Azuaje F 2009 GRIP: a web-based system for constructing gold standard datasets for protein-protein interaction prediction Source Code Biol. Med. 4 2
121. Chen X W, Jeong J C and Dermyer P 2010 KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions Nucleic Acids Res 39 D750-4
122. Sharan R, Suthram S, Kelley R M, Kuhn T, McCuine S, Uetz P, Sittler T, Karp R M and Ideker T 2005 Conserved patterns of protein interaction in multiple species Proc Natl. Acad. Sci. USA 102 1974-9 (Pubitemid 40261997)
123. Kanehisa M et al 2008 KEGG for linking genomes to life and the environment Nucleic Acids Res. 36 D480-4
124. Thomas P D, Campbell M J, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A and Narechania A 2003 PANTHER: a library of protein families and subfamilies indexed by function Genome Res. 13 2129-41 (Pubitemid 37161770)
125. Ioannidis J P 2007 Why most published research findings are false: author's reply to Goodman and Greenland PLoS Med. 4 e215
126. Pfeiffer T, Rand D G and Dreber A 2009 Decision-making in research tasks with sequential testing PLoS ONE 4 e4607
127. Neumann B et al 2010 Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes Nature 464 721-7
128. Uetz P et al 2000 A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 403 623-7 (Pubitemid 30103994)
129. Russell R B and Aloy P 2008 Targeting and tinkering with interaction networks Nat. Chem. Biol. 4 666-73
130. Hart G T, Ramani A K and Marcotte E M 2006 How complete are current yeast and human protein-interaction networks? Genome Biol. 7 120
131. Lefebvre C et al 2010 A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers Mol. Syst. Biol. 6 377
132. Warde-Farley D et al 2010 The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function Nucleic Acids Res. 38 W214-20
133. Lefebvre C, Lim W K, Basso K, dalla-Favera R and Califano A 2007 A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells Lect. Notes Bioinformatics (LNCS) 4532 42-56
134. Krogan N J et al 2006 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 440 637-43
135. Gavin A C et al 2006 Proteome survey reveals modularity of the yeast cell machinery Nature 440 631-6
136. Li S et al 2004 A map of the interactome network of the metazoan C. elegans Science 303 540-3 (Pubitemid 38120855)
137. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M and Sakaki Y 2001 A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc. Natl Acad. Sci. USA 98 4569-74 (Pubitemid 32295017)
138. Giot L et al 2003 A protein interaction map of Drosophila melanogaster Science 302 1727-36 (Pubitemid 37505730)
139. Wu D et al 2009 A phylogeny-driven genomic encyclopaedia of bacteria and archaea Nature 462 1056-60
140. Kahlem P and Birney E 2007 ENFIN a network to enhance integrative systems biology Ann. New York Acad. Sci. 1115 23-31 (Pubitemid 350134805)