Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments

Molecular and Cellular Proteomics

Volumn 12, Issue 1, 2013, Pages 1-13

  Armean, Irina M ^a   Lilley, Kathryn S ^a   Trotters, Matthew W B ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b Celgene Institute for Translational Research Europe CITRE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AFFINITY PURIFICATION; ALGORITHM; ANALYTIC METHOD; CALCULATION; COMPLEX FORMATION; COMPUTER MODEL; COMPUTER PROGRAM; HUMAN; MACHINE LEARNING; MASS SPECTROMETRY; MEASUREMENT ACCURACY; METHODOLOGY; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; REPRODUCIBILITY; REVIEW; SCORING SYSTEM;

ALGORITHMS; ANIMALS; BACTERIA; CHROMATOGRAPHY, AFFINITY; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; MASS SPECTROMETRY; METHIONINE; MULTIPROTEIN COMPLEXES; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE;

EID: 84871865189     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.R112.019554     Document Type: Review

References (170)

1. Lee, S. W., Berger, S. J., Martinović, S., Pasa-Tolić, L., Anderson, G. A., Shen, Y., Zhao, R., and Smith, R. D. (2002) Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR. Proc. Natl. Acad. Sci. U. S. A. 99, 5942-5947 (Pubitemid 34493244)
2. 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, 825-831
3. Alberts, B. (1998) The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists. Cell 92, 291-294
4. Razick, S., Magklaras, G., and Donaldson, I. M. (2008) iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics 9, 405
5. Babu, M., Vlasblom, J., Pu, S., Guo, X., Graham, C., Bean, B. D. M., Burston, H. E., Vizeacoumar, F. J., Snider, J., Phanse, S., Fong, V., Tam, Y. Y. C., Davey, M., Hnatshak, O., Bajaj, N., Chandran, S., Punna, T., Christopolous, C., Wong, V., Yu, A., Zhong, G., Li, J., Stagljar, I., Conibear, E., Wodak, S. J., Emili, A., and Greenblatt, J. F. (2012) Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature [online] http://www.ncbi.nlm.nih.gov/pubmed/22940862 (Accessed September 6, 2012).
6. Havugimana, P. C., Hart, G. T., Nepusz, T., Yang, H., Turinsky, A. L., Li, Z., Wang, P. I., Boutz, D. R., Fong, V., Phanse, S., Babu, M., Craig, S. A., Hu, P., Wan, C., Vlasblom, J., Dar, V.-N., Bezginov, A., Clark, G. W., Wu, G. C., Wodak, S. J., Tillier, E. R. M., Paccanaro, A., Marcotte, E. M., and Emili, A. (2012) A Census of Human Soluble Protein Complexes. Cell 150, 1068-1081
7. Chien, C. T., Bartel, P. L., Sternglanz, R., and 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. U.S.A. 88, 9578-9582 (Pubitemid 21915674)
8. Tavernier, J., Eyckerman, S., Lemmens, I., Van der Heyden, J., Vandekerckhove, J., and Van Ostade, X. (2002) MAPPIT: a cytokine receptorbased two-hybrid method in mammalian cells. Clin. Exp. Allergy 32, 1397-1404 (Pubitemid 35278904)
9. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J. M. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (Pubitemid 30103994)
10. 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. U.S.A. 98, 4569-4574 (Pubitemid 32295017)
11. Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C. E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C. A., Finley, R. L., White, K. P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R. A., McKenna, M. P., Chant, J., and Rothberg, J. M. (2003) A protein interaction map of Drosophila melanogaster. Science 302, 1727-1736 (Pubitemid 37505730)
12. Deane, C. M., Salwiński, L., Xenarios, I., and Eisenberg, D. (2002) Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol. Cell. Proteomics 1, 349-356
13. Sprinzak, E., Sattath, S., and Margalit, H. (2003) How reliable are experimental protein-protein interaction data? J. Mol. Biol. 327, 919-923 (Pubitemid 36363701)
14. Fields, S. (2005) High-throughput two-hybrid analysis. The promise and the peril. FEBS J. 272, 5391-5399
15. Rajagopala, S. V., Hughes, K. T., and Uetz, P. (2009) Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins. Proteomics 9, 5296-5302
16. Barrios-Rodiles, M., Brown, K. R., Ozdamar, B., Bose, R., Liu, Z., Donovan, R. S., Shinjo, F., Liu, Y., Dembowy, J., Taylor, I. W., Luga, V., Przulj, N., Robinson, M., Suzuki, H., Hayashizaki, Y., Jurisica, I., and Wrana, J. L. (2005) High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307, 1621-1625 (Pubitemid 40354744)
17. Eyckerman, S., Verhee, A., der Heyden, J. V., Lemmens, I., Ostade, X. V., Vandekerckhove, J., and Tavernier, J. (2001) Design and application of a cytokine-receptor-based interaction trap. Nat. Cell Biol. 3, 1114-1119 (Pubitemid 33130462)
18. Nyfeler, B., Michnick, S. W., and Hauri, H. P. (2005) Capturing protein interactions in the secretory pathway of living cells. Proc. Natl. Acad. Sci. U.S.A. 102, 6350-6355 (Pubitemid 40617446)
19. Ramachandran, N., Raphael, J. V., Hainsworth, E., Demirkan, G., Fuentes, M. G., Rolfs, A., Hu, Y., and LaBaer, J. (2008) Next-generation high-density self-assembling functional protein arrays. Nat. Methods 5, 535-538 (Pubitemid 351761761)
20. Braun, P., Tasan, M., Dreze, M., Barrios-Rodiles, M., Lemmens, I., Yu, H., Sahalie, J. M., Murray, R. R., Roncari, L., de Smet, A. S., Venkatesan, K., Rual, J. F., Vandenhaute, J., Cusick, M. E., Pawson, T., Hill, D. E., Tavernier, J., Wrana, J. L., Roth, F. P., and Vidal, M. (2009) An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods 6, 91-97
21. Venkatesan, K., Rual, J. F., Vazquez, A., Stelzl, U., Lemmens, I., Hirozane- Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K. I., Yildirim, M. A., Simonis, N., Heinzmann, K., Gebreab, F., Sahalie, J. M., Cevik, S., Simon, C., de Smet, A. S., Dann, E., Smolyar, A., Vinayagam, A., Yu, H., Szeto, D., Borick, H., Dricot, A., Klitgord, N., Murray, R. R., Lin, C., Lalowski, M., Timm, J., Rau, K., Boone, C., Braun, P., Cusick, M. E., Roth, F. P., Hill, D. E., Tavernier, J., Wanker, E. E., Barabási, A. L., and Vidal, M. (2009) An empirical framework for binary interactome mapping. Nat. Methods 6, 83-90
22. Chen, Y.-C., Rajagopala, S. V., Stellberger, T., and Uetz, P. (2010) Exhaustive benchmarking of the yeast two-hybrid system. Nat. Methods 7, 667-668
23. Vazquez, A., Rual, J. F., and Venkatesan, K. (2011) Quality control methodology for high-throughput protein-protein interaction screening. Methods Mol. Biol. 781, 279-294
24. MacBeath, G., and Schreiber, S. L. (2000) Printing proteins as microarrays for high-throughput function determination. Science 289, 1760-1763
25. Kung, L. A., and Snyder, M. (2006) Proteome chips for whole-organism assays. Nat. Rev. Mol. Cell Biol. 7, 617-622 (Pubitemid 44325353)
26. Tessler, L. A., and Mitra, R. D. (2011) Sensitive single-molecule protein quantification and protein complex detection in a microarray format. Proteomics 11, 4731-4735
27. Shoemaker, B. A., and Panchenko, A. R. (2007) Deciphering proteinprotein interactions. Part I. Experimental techniques and databases. PLoS Comput. Biol. 3, e42
28. Collins, M. O., and Choudhary, J. S. (2008) Mapping multiprotein complexes by affinity purification and mass spectrometry. Curr. Opin. Biotechnol. 19, 324-330
29. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., and Séraphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030-1032 (Pubitemid 29474865)
30. Puig, O., Caspary, F., Rigaut, G., Rutz, B., Bouveret, E., Bragado-Nilsson, E., Wilm, M., and Séraphin, B. (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218-229 (Pubitemid 32846428)
31. Rees, J. S., Lowe, N., Armean, I. M., Roote, J., Johnson, G., Drummond, E., Spriggs, H., Ryder, E., Russell, S., St Johnston, D., and Lilley, K. S. (2011) In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry. Mol. Cell. Proteomics 10, M110.002386
32. Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., 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, J. M., Kuster, B., Bork, P., Russell, R. B., and Superti-Furga, G. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636
33. Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A. P., Punna, T., Peregrín-Alvarez, J. M., Shales, M., Zhang, X., Davey, M., Robinson, M. D., Paccanaro, A., Bray, J. E., Sheung, A., Beattie, B., Richards, D. P., Canadien, V., Lalev, A., Mena, F., Wong, P., Starostine, A., Canete, M. M., Vlasblom, J., Wu, S., Orsi, C., Collins, S. R., Chandran, S., Haw, R., Rilstone, J. J., Gandi, K., Thompson, N. J., Musso, G., St Onge, P., Ghanny, S., Lam, M. H. Y., Butland, G., Altaf-Ul, A. M., Kanaya, S., Shilatifard, A., O'Shea, E., Weissman, J. S., Ingles, C. J., Hughes, T. R., Parkinson, J., Gerstein, M., Wodak, S. J., Emili, A., and Greenblatt, J. F. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643
34. Polanowska, J., Martin, J. S., Fisher, R., Scopa, T., Rae, I., and Boulton, S. J. (2004) Tandem immunoaffinity purification of protein complexes from Caenorhabditis elegans. BioTechniques 36, 778- 780, 782
35. Butland, G., Peregrín-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J., and Emili, A. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531-537 (Pubitemid 40204311)
36. Veraksa, A., Bauer, A., and Artavanis-Tsakonas, S. (2005) Analyzing protein complexes in Drosophila with tandem affinity purification-mass spectrometry. Dev. Dyn. 232, 827-834 (Pubitemid 40315300)
37. Ewing, R. M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., McBroom- Cerajewski, L., Robinson, M. D., O'Connor, L., Li, M., Taylor, R., Dharsee, M., Ho, Y., Heilbut, A., Moore, L., Zhang, S., Ornatsky, O., Bukhman, Y. V., Ethier, M., Sheng, Y., Vasilescu, J., Abu-Farha, M., Lambert, J. P., Duewel, H. S., Stewart, I. I., Kuehl, B., Hogue, K., Colwill, K., Gladwish, K., Muskat, B., Kinach, R., Adams, S. L., Moran, M. F., Morin, G. B., Topaloglou, T., and Figeys, D. (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3, 89
38. Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M., Foster, L. J., and Mann, M. (2003) A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21, 315-318 (Pubitemid 36314817)
39. Ranish, J. A., Yi, E. C., Leslie, D. M., Purvine, S. O., Goodlett, D. R., Eng, J., and Aebersold, R. (2003) The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33, 349-355 (Pubitemid 36278851)
40. Himeda, C. L., Ranish, J. A., Angello, J. C., Maire, P., Aebersold, R., and Hauschka, S. D. (2004) Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer. Mol. Cell. Biol. 24, 2132-2143 (Pubitemid 38248951)
41. Ranish, J. A., Hahn, S., Lu, Y., Yi, E. C., Li, X., Eng, J., and Aebersold, R. (2004) Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat. Genet. 36, 707-713 (Pubitemid 38886631)
42. Brand, M., Ranish, J. A., Kummer, N. T., Hamilton, J., Igarashi, K., Francastel, C., Chi, T. H., Crabtree, G. R., Aebersold, R., and Groudine, M. (2004) Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat Struct Mol Biol 11, 73-80 (Pubitemid 38173444)
43. Kratchmarova, I., Blagoev, B., Haack-Sorensen, M., Kassem, M., and Mann, M. (2005) Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science 308, 1472-1477 (Pubitemid 40791302)
44. Mewes, H. W., Ruepp, A., Theis, F., Rattei, T., Walter, M., Frishman, D., Suhre, K., Spannagl, M., Mayer, K. F. X., Stümpflen, V., and Antonov, A. (2011) MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res. 39, D220-224
45. Kühner, S., van Noort, V., Betts, M. J., 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, A. S., Russell, R. B., Serrano, L., Bork, P., and Gavin, A. C. (2009) Proteome organization in a genome-reduced bacterium. Science 326, 1235-1240
46. Gavin, A. C., Maeda, K., and Kühner, S. (2011) Recent advances in charting protein-protein interaction: mass spectrometry-based approaches. Curr. Opin. Biotechnol. 22, 42-49
47. Glatter, T., Wepf, A., Aebersold, R., and Gstaiger, M. (2009) An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol. Syst. Biol. 5, 237
48. Chang, I. F. (2006) Mass spectrometry-based proteomic analysis of the epitope-tag affinity purified protein complexes in eukaryotes. Proteomics 6, 6158-6166
49. Martín, M. L., and Busconi, L. (2000) Membrane localization of a rice calcium-dependent protein kinase (CDPK) is mediated by myristoylation and palmitoylation. Plant J 24, 429-435 (Pubitemid 32003668)
50. Kristensen, A. R., Gsponer, J., and Foster, L. J. (2012) A high-throughput approach for measuring temporal changes in the interactome. Nat. Methods 9, 907-909
51. Wodak, S. J., Pu, S., Vlasblom, J., and Séraphin, B. (2009) Challenges and rewards of interaction proteomics. Mol. Cell. Proteomics 8, 3-18
52. Oeljeklaus, S., Reinartz, B. S., Wolf, J., Wiese, S., Tonillo, J., Podwojski, K., Kuhlmann, K., Stephan, C., Meyer, H. E., Schliebs, W., Brocard, C., Erdmann, R., and Warscheid, B. (2012) Identification of core components and transient interactors of the peroxisomal importomer by dualtrack stable isotope labeling with amino acids in cell culture analysis. J. Proteome Res. 11, 2567-2580
53. Selbach, M., and Mann, M. (2006) Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat. Methods 3, 981-983 (Pubitemid 44782696)
54. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386
55. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D. J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154-1169
56. Schmidt, A., Kellermann, J., and Lottspeich, F. (2005) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5, 4-15 (Pubitemid 40189632)
57. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope- coded affinity tags. Nat. Biotechnol. 17, 994-999 (Pubitemid 29474856)
58. Sardiu, M. E., Cai, Y., Jin, J., Swanson, S. K., Conaway, R. C., Conaway, J. W., Florens, L., and Washburn, M. P. (2008) Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc. Natl. Acad. Sci. U.S.A. 105, 1454-1459 (Pubitemid 351346535)
59. Trinkle-Mulcahy, L. (2012) Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry. Proteomics 12, 1623-1638
60. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567 (Pubitemid 30007252)
61. Eng, J. K., McCormack, A. L., and Yates, J. R. (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
62. Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467 (Pubitemid 38931421)
63. Kapp, E. A., Schütz, F., Connolly, L. M., Chakel, J. A., Meza, J. E., Miller, C. A., Fenyo, D., Eng, J. K., Adkins, J. N., Omenn, G. S., and Simpson, R. J. (2005) An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics 5, 3475-3490 (Pubitemid 41192052)
64. Boutilier, K., Ross, M., Podtelejnikov, A. V., Orsi, C., Taylor, R., Taylor, P., and Figeys, D. (2005) Comparison of different search engines using validated MS/MS test datasets. Anal. Chim. Acta 534, 11-20 (Pubitemid 40410550)
65. Balgley, B. M., Laudeman, T., Yang, L., Song, T., and Lee, C. S. (2007) Comparative evaluation of tandem MS search algorithms using a targetdecoy search strategy. Mol. Cell. Proteomics 6, 1599-1608 (Pubitemid 47506170)
66. Nesvizhskii, A. I., Vitek, O., and Aebersold, R. (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 4, 787-797 (Pubitemid 350055575)
67. Reiter, L., Claassen, M., Schrimpf, S. P., Jovanovic, M., Schmidt, A., Buhmann, J. M., Hengartner, M. O., and Aebersold, R. (2009) Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol. Cell. Proteomics 8, 2405-2417
68. Yu, W., Taylor, J. A., Davis, M. T., Bonilla, L. E., Lee, K. A., Auger, P. L., Farnsworth, C. C., Welcher, A. A., and Patterson, S. D. (2010) Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines. Proteomics 10, 1172-1189
69. Stengel, F., Aebersold, R., and Robinson, C. V. (2012) Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol. Cell. Proteomics 11, R111.014027
70. Sohn, C. H., Agnew, H. D., Lee, J. E., Sweredoski, M. J., Graham, R. L. J., Smith, G. T., Hess, S., Czerwieniec, G., Loo, J. A., Heath, J. R., Deshaies, R. J., and Beauchamp, J. L. (2012) Designer reagents for mass spectrometry-based proteomics: clickable cross-linkers for elucidation of protein structures and interactions. Anal. Chem. 84, 2662-2669
71. Smialowski, P., Pagel, P., Wong, P., Brauner, B., Dunger, I., Fobo, G., Frishman, G., Montrone, C., Rattei, T., Frishman, D., and Ruepp, A. (2010) The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res. 38, D540-544
72. Bader, G. D., Cary, M. P., and Sander, C. (2006) Pathguide: a pathway resource list. Nucleic Acids Res. 34, D504-506
73. Keshava Prasad, T. S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A., Balakrishnan, L., Marimuthu, A., Banerjee, S., Somanathan, D. S., Sebastian, A., Rani, S., Ray, S., Harrys Kishore, C. J., Kanth, S., Ahmed, M., Kashyap, M. K., Mohmood, R., Ramachandra, Y. L., Krishna, V., Rahiman, B. A., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R., and Pandey, A. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res. 37, D767-772
74. Kerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackes-Carter, F., Chen, C., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U., Jandrasits, C., Jimenez, R. C., Khadake, J., Mahadevan, U., Masson, P., Pedruzzi, I., Pfeiffenberger, E., Porras, P., Raghunath, A., Roechert, B., Orchard, S., and Hermjakob, H. (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res. 40, D841-846
75. Licata, L., Briganti, L., Peluso, D., Perfetto, L., Iannuccelli, M., Galeota, E., Sacco, F., Palma, A., Nardozza, A. P., Santonico, E., Castagnoli, L., and Cesareni, G. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 40, D857-861
76. Salwinski, L., Miller, C. S., Smith, A. J., Pettit, F. K., Bowie, J. U., and Eisenberg, D. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 32, D449-451 (Pubitemid 38081696)
77. Bader, G. D., Betel, D., and Hogue, C. W. V. (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 248-250 (Pubitemid 36150376)
78. Stark, C., Breitkreutz, B.-J., Chatr-Aryamontri, A., Boucher, L., Oughtred, R., Livstone, M. S., Nixon, J., Van Auken, K., Wang, X., Shi, X., Reguly, T., Rust, J. M., Winter, A., Dolinski, K., and Tyers, M. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 39, D698-704
79. Güldener, U., Münsterkötter, M., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H.-W., and Stümpflen, V. (2006) MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 34, D436-441
80. Lynn, D. J., Winsor, G. L., Chan, C., Richard, N., Laird, M. R., Barsky, A., Gardy, J. L., Roche, F. M., Chan, T. H. W., Shah, N., Lo, R., Naseer, M., Que, J., Yau, M., Acab, M., Tulpan, D., Whiteside, M. D., Chikatamarla, A., Mah, B., Munzner, T., Hokamp, K., Hancock, R. E. W., and Brinkman, F. S. L. (2008) InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 4, 218
81. Cohen, A. M., and Hersh, W. R. (2005) A survey of current work in biomedical text mining. Briefings Bioinformatics 6, 57-71 (Pubitemid 40528580)
82. Polajnar, T., Damoulas, T., and Girolami, M. (2011) Protein interaction sentence detection using multiple semantic kernels. J. Biomed. Semantics 2, 1
83. Turinsky, A. L., Razick, S., Turner, B., Donaldson, I. M., and Wodak, S. J. (2010) Literature curation of protein interactions: measuring agreement across major public databases. Database 2010, baq026
84. Cusick, M. E., Yu, H., Smolyar, A., Venkatesan, K., Carvunis, A.-R., Simonis, N., Rual, J.-F., Borick, H., Braun, P., Dreze, M., Vandenhaute, J., Galli, M., Yazaki, J., Hill, D. E., Ecker, J. R., Roth, F. P., and Vidal, M. (2009) Literature-curated protein interaction datasets. Nat. Methods 6, 39-46
85. Salwinski, L., Licata, L., Winter, A., Thorneycroft, D., Khadake, J., Ceol, A., Aryamontri, A. C., Oughtred, R., Livstone, M., Boucher, L., Botstein, D., Dolinski, K., Berardini, T., Huala, E., Tyers, M., Eisenberg, D., Cesareni, G., and Hermjakob, H. (2009) Recurated protein interaction datasets. Nat. Methods 6, 860-861
86. Cusick, M. E., Yu, H., Smolyar, A., Venkatesan, K., Carvunis, A.-R., Simonis, N., Rual, J.-F., Borick, H., Braun, P., Dreze, M., Vandenhaute, J., Galli, M., Yazaki, J., Hill, D. E., Ecker, J. R., Roth, F. P., and Vidal, M. (2009) Addendum: Literature-curated protein interaction datasets. Nat. Methods 6, 934-935
87. Orchard, S., Kerrien, S., Abbani, S., Aranda, B., Bhate, J., Bidwell, S., Bridge, A., Briganti, L., Brinkman, F. S. L., Brinkman, F., Cesareni, G., Chatr-aryamontri, A., Chautard, E., Chen, C., Dumousseau, M., Goll, J., Hancock, R. E., Hancock, R., Hannick, L. I., Jurisica, I., Khadake, J., Lynn, D. J., Mahadevan, U., Perfetto, L., Raghunath, A., Ricard-Blum, S., Roechert, B., Salwinski, L., Stümpflen, V., Tyers, M., Uetz, P., Xenarios, I., and Hermjakob, H. (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods 9, 345-350
88. Kerrien, S., Orchard, S., Montecchi-Palazzi, L., Aranda, B., Quinn, A. F., Vinod, N., Bader, G. D., Xenarios, I., Wojcik, J., Sherman, D., Tyers, M., Salama, J. J., Moore, S., Ceol, A., Chatr-Aryamontri, A., Oesterheld, M., Stümpflen, V., Salwinski, L., Nerothin, J., Cerami, E., Cusick, M. E., Vidal, M., Gilson, M., Armstrong, J., Woollard, P., Hogue, C., Eisenberg, D., Cesareni, G., Apweiler, R., and Hermjakob, H. (2007) Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 5, 44
89. Aranda, B., Blankenburg, H., Kerrien, S., Brinkman, F. S., Ceol, A., Chautard, E., Dana, J. M., De Las Rivas, J., Dumousseau, M., Galeota, E., Gaulton, A., Goll, J., Hancock, R. E., Isserlin, R., Jimenez, R. C., Kerssemakers, J., Khadake, J., Lynn, D. J., Michaut, M., O'Kelly, G., Ono, K., Orchard, S., Prieto, C., Razick, S., Rigina, O., Salwinski, L., Simonovic, M., Velankar, S., Winter, A., Wu, G., Bader, G. D., Cesareni, G., Donaldson, I. M., Eisenberg, D., Kleywegt, G. J., Overington, J., Ricard- Blum, S., Tyers, M., Albrecht, M., and Hermjakob, H. (2011) PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat. Methods 8, 528-529
90. Turner, B., Razick, S., Turinsky, A. L., Vlasblom, J., Crowdy, E. K., Cho, E., Morrison, K., Donaldson, I. M., and Wodak, S. J. (2010) iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database 2010, baq023
91. Sowa, M. E., Bennett, E. J., Gygi, S. P., and Harper, J. W. (2009) Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389-403
92. Behrends, C., Sowa, M. E., Gygi, S. P., and Harper, J. W. (2010) Network organization of the human autophagy system. Nature 466, 68-76
93. Christianson, J. C., Olzmann, J. A., Shaler, T. A., Sowa, M. E., Bennett, E. J., Richter, C. M., Tyler, R. E., Greenblatt, E. J., Harper, J. W., and Kopito, R. R. (2012) Defining human ERAD networks through an integrative mapping strategy. Nat. Cell Biol. 14, 93-105
94. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G., Mendoza, A., Sevinsky, J. R., Resing, K. A., and Ahn, N. G. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4, 1487-1502 (Pubitemid 41555475)
95. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., and Kuster, B. (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389, 1017-1031 (Pubitemid 47482251)
96. Barton, S. J., and Whittaker, J. C. (2009) Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors. Mass Spectrom. Rev. 28, 177-187
97. Tabb, D. L., Vega-Montoto, L., Rudnick, P. A., Variyath, A. M., Ham, A. J. L., Bunk, D. M., Kilpatrick, L. E., Billheimer, D. D., Blackman, R. K., Cardasis, H. L., Carr, S. A., Clauser, K. R., Jaffe, J. D., Kowalski, K. A., Neubert, T. A., Regnier, F. E., Schilling, B., Tegeler, T. J., Wang, M., Wang, P., Whiteaker, J. R., Zimmerman, L. J., Fisher, S. J., Gibson, B. W., Kinsinger, C. R., Mesri, M., Rodriguez, H., Stein, S. E., Tempst, P., Paulovich, A. G., Liebler, D. C., and Spiegelman, C. (2010) Repeatability and reproducibility in proteomic identifications by liquid chroma-tography- tandem mass spectrometry. J. Proteome Res. 9, 761-776
98. Choi, H., Larsen, B., Lin, Z.-Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z. S., Tyers, M., Gingras, A.-C., and Nesvizhskii, A. I. (2011) SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat. Methods 8, 70-73
99. Breitkreutz, A., Choi, H., Sharom, J. R., Boucher, L., Neduva, V., Larsen, B., Lin, Z. Y., Breitkreutz, B. J., Stark, C., Liu, G., Ahn, J., Dewar-Darch, D., Reguly, T., Tang, X., Almeida, R., Qin, Z. S., Pawson, T., Gingras, A. C., Nesvizhskii, A. I., and Tyers, M. (2010) A global protein kinase and phosphatase interaction network in yeast. Science 328, 1043-1046
100. Choi, H., Glatter, T., Gstaiger, M., and Nesvizhskii, A. I. (2012) SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments. J. Proteome Res. 11, 2619-2624
101. Nesvizhskii, A. I. (2012) Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 12, 1639-1655
102. Guruharsha, K. G., Rual, J. F., Zhai, B., Mintseris, J., Vaidya, P., Vaidya, N., Beekman, C., Wong, C., Rhee, D. Y., Cenaj, O., McKillip, E., Shah, S., Stapleton, M., Wan, K. H., Yu, C., Parsa, B., Carlson, J. W., Chen, X., Kapadia, B., VijayRaghavan, K., Gygi, S. P., Celniker, S. E., Obar, R. A., and Artavanis-Tsakonas, S. (2011) A protein complex network of Drosophila melanogaster. Cell 147, 690-703
103. 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
104. Enright, A. J., Van Dongen, S., and Ouzounis, C. A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575-1584 (Pubitemid 34679732)
105. Huang, da, W., Sherman, B. T., and Lempicki, R. A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13
106. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40, D109-114
107. Graveley, B. R., Brooks, A. N., Carlson, J. W., Duff, M. O., Landolin, J. M., Yang, L., Artieri, C. G., van Baren, M. J., Boley, N., Booth, B. W., Brown, J. B., Cherbas, L., Davis, C. A., Dobin, A., Li, R., Lin, W., Malone, J. H., Mattiuzzo, N. R., Miller, D., Sturgill, D., Tuch, B. B., Zaleski, C., Zhang, D., Blanchette, M., Dudoit, S., Eads, B., Green, R. E., Hammonds, A., Jiang, L., Kapranov, P., Langton, L., Perrimon, N., Sandler, J. E., Wan, K. H., Willingham, A., Zhang, Y., Zou, Y., Andrews, J., Bickel, P. J., Brenner, S. E., Brent, M. R., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Oliver, B., and Celniker, S. E. (2011) The developmental transcriptome of Drosophila melanogaster. Nature 471, 473-479
108. Collins, S. R., Kemmeren, P., Zhao, X. C., Greenblatt, J. F., Spencer, F., Holstege, F. C. P., Weissman, J. S., and Krogan, N. J. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics 6, 439-450 (Pubitemid 46554539)
109. Lavallée-Adam, M., Cloutier, P., Coulombe, B., and Blanchette, M. (2011) Modeling contaminants in AP-MS/MS experiments. J. Proteome Res. 10, 886-895
110. Cloutier, P., Al-Khoury, R., Lavallée-Adam, M., Faubert, D., Jiang, H., Poitras, C., Bouchard, A., Forget, D., Blanchette, M., and 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
111. Turck, C. W., Falick, A. M., Kowalak, J. A., Lane, W. S., Lilley, K. S., Phinney, B. S., Weintraub, S. T., Witkowska, H. E., and Yates, N. A. (2007) The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 study: relative protein quantitation. Mol. Cell. Proteomics 6, 1291-1298 (Pubitemid 47365429)
112. Falick, A. M., Lane, W. S., Lilley, K. S., MacCoss, M. J., Phinney, B. S., Sherman, N. E., Weintraub, S. T., Witkowska, H. E., and Yates, N. A. (2011) ABRF-PRG07: advanced quantitative proteomics study. J. Biomol. Tech. 22, 21-26
113. Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteomewide protein quantification. Nat. Biotechnol. 26, 1367-1372
114. Hubner, N. C., and Mann, M. (2011) Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC). Methods 53, 453-459
115. Pearson (1901) On lines and planes of closest fit to systems of points in space. Philos. Mag. 2, 559-572
116. Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J. R., McGovern, K. E., Clarke, S. C., Shales, M., Mercenne, G., Pache, L., Li, K., Hernandez, H., Jang, G. M., Roth, S. L., Akiva, E., Marlett, J., Stephens, M., D'Orso, I., Fernandes, J., Fahey, M., Mahon, C., O'Donoghue, A. J., Todorovic, A., Morris, J. H., Maltby, D. A., Alber, T., Cagney, G., Bushman, F. D., Young, J. A., Chanda, S. K., Sundquist, W. I., Kortemme, T., Hernandez, R. D., Craik, C. S., Burlingame, A., Sali, A., Frankel, A. D., and Krogan, N. J. (2012) Global landscape of HIV-human protein complexes. Nature 481, 365-370
117. Ceol, A., Chatr Aryamontri, A., Licata, L., Peluso, D., Briganti, L., Perfetto, L., Castagnoli, L., and Cesareni, G. (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res. 38, D532-539
118. Ostlund, G., Schmitt, T., Forslund, K., Köstler, T., Messina, D. N., Roopra, S., Frings, O., and Sonnhammer, E. L. L. (2010) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38, D196-203
119. Orchard, S., Salwinski, L., Kerrien, S., Montecchi-Palazzi, L., Oesterheld, M., Stümpflen, V., Ceol, A., Chatr-aryamontri, A., Armstrong, J., Woollard, P., Salama, J. J., Moore, S., Wojcik, J., Bader, G. D., Vidal, M., Cusick, M. E., Gerstein, M., Gavin, A. C., Superti-Furga, G., Greenblatt, J., Bader, J., Uetz, P., Tyers, M., Legrain, P., Fields, S., Mulder, N., Gilson, M., Niepmann, M., Burgoon, L., De Las Rivas, J., Prieto, C., Perreau, V. M., Hogue, C., Mewes, H. W., Apweiler, R., Xenarios, I., Eisenberg, D., Cesareni, G., and Hermjakob, H. (2007) The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat. Biotechnol. 25, 894-898 (Pubitemid 47236917)
120. Deng, M., Mehta, S., Sun, F., and Chen, T. (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Res. 12, 1540-1548 (Pubitemid 35175092)
121. Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., Jensen, L. J., and von Mering, C. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39, D561-568
122. Huynen, M. A., Snel, B., von Mering, C., and Bork, P. (2003) Function prediction and protein networks. Curr Opin Cell Biol. 15, 191-198 (Pubitemid 36332194)
123. Saric, J., Jensen, L. J., Ouzounova, R., Rojas, I., and Bork, P. (2006) Extraction of regulatory gene/protein networks from Medline. Bioinformatics 22, 645-650
124. von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., and Snel, B. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31, 258-261 (Pubitemid 36150379)
125. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D., and Maltsev, N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. U. S. A. 96, 2896-2901 (Pubitemid 29148815)
126. Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P., and von Mering, C. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37, D412-416
127. Enright, A. J., Iliopoulos, I., Kyrpides, N. C., and Ouzounis, C. A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86-90
128. Snel, B., Bork, P., and Huynen, M. (2000) Genome evolution. Gene fusion versus gene fission. Trends Genet. 16, 9-11 (Pubitemid 30062226)
129. Yanai, I., Derti, A., and DeLisi, C. (2001) Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc. Natl. Acad. Sci. U.S.A. 98, 7940-7945 (Pubitemid 32642666)
130. Pellegrini, M. (2012) Using phylogenetic profiles to predict functional relationships. Methods Mol. Biol. 804, 167-177
131. Enright, A. J., and Ouzounis, C. A. (2001) Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol. 2, RESEARCH0034
132. Enright, A. J., Kunin, V., and Ouzounis, C. A. (2003) Protein families and TRIBES in genome sequence space. Nucleic Acids Res. 31, 4632-4638 (Pubitemid 37441823)
133. Lee, J. M., and Sonnhammer, E. L. L. (2003) Genomic gene clustering analysis of pathways in eukaryotes. Genome Res. 13, 875-882 (Pubitemid 36621748)
134. Suhre, K., and Claverie, J. M. (2004) FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. Nucleic Acids Res. 32, D273-276 (Pubitemid 38081655)
135. Blumenthal, T. (2004) Operons in eukaryotes. Brief Funct. Genomic Proteomic 3, 199-211
136. Hurst, L. D., Pál, C., and Lercher, M. J. (2004) The evolutionary dynamics of eukaryotic gene order. Nat. Rev. Genet. 5, 299-310 (Pubitemid 38435625)
137. Michalak, P. (2008) Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91, 243-248
138. Koonin, E. V. (2009) Evolution of genome architecture. Int. J. Biochem. Cell Biol. 41, 298-306
139. Singh, S., and Wall, D. P. (2008) Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function. Evol Bioinform Online 4, 217-223
140. Huynen, M., Snel, B., Lathe, W., 3rd, and Bork, P. (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10, 1204-1210
141. von Mering, C., Jensen, L. J., Snel, B., Hooper, S. D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M. A., and Bork, P. (2005) STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33, D433-437 (Pubitemid 40207910)
142. Jensen, L. J., Lagarde, J., von Mering, C., and Bork, P. (2004) ArrayProspector: a web resource of functional associations inferred from microarray expression data. Nucleic Acids Res. 32, W445-448 (Pubitemid 38997374)
143. Donoho, D. L. (2000) High-Dimensional Data Analysis: the curses and blessings of dimensionality. Technical Review. Stanford University Department of Statistics
144. 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, 249-255 (Pubitemid 37248749)
145. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (Pubitemid 30047768)
146. Haw, R. A., Croft, D., Yung, C. K., Ndegwa, N., D'Eustachio, P., Hermjakob, H., and Stein, L. D. (2011) The Reactome BioMart. Database 2011, bar031
147. von Mering, C., Jensen, L. J., Kuhn, M., Chaffron, S., Doerks, T., Krüger, B., Snel, B., and Bork, P. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35, D358-362 (Pubitemid 46056231)
148. Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Karra, K., Krieger, C. J., Miyasato, S. R., Nash, R. S., Park, J., Skrzypek, M. S., Simison, M., Weng, S., and Wong, E. D. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 40, D700-705
149. McKusick, V. A. (1998) Mendelian inheritance in man. A catalog of human genes and genetic disorders, 12th Ed., Johns Hopkins University Press, Baltimore, MD
150. Alexeyenko, A., Schmitt, T., Tjärnberg, A., Guala, D., Frings, O., and Sonnhammer, E. L. L. (2012) Comparative interactomics with Funcoup 2.0. Nucleic Acids Res. 40, D821-828
151. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 (Pubitemid 30257031)
152. Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S., Wernerus, H., Björling, L., and Ponten, F. (2010) Towards a knowledge-based Human Protein Atlas. Nat. Biotechnol. 28, 1248-1250
153. Hallikas, O., Palin, K., Sinjushina, N., Rautiainen, R., Partanen, J., Ukkonen, E., and Taipale, J. (2006) Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, 47-59 (Pubitemid 43069309)
154. Gupta, R., Bhattacharyya, A., Agosto-Perez, F. J., Wickramasinghe, P., and Davuluri, R. V. (2011) MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. Nucleic Acids Res. 39, D92-97
155. Yu, H., Luscombe, N. M., Lu, H. X., Zhu, X., Xia, Y., Han, J. D., Bertin, N., Chung, S., Vidal, M., and Gerstein, M. (2004) Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 14, 1107-1118 (Pubitemid 38811547)
156. Kozomara, A., and Griffiths-Jones, S. (2011) miRBase: integrating micro- RNA annotation and deep-sequencing data. Nucleic Acids Res. 39, D152-157
157. Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., Koh, J. L., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. Y., Liang, W., Marback, M., Paw, J., San Luis, B. J., Shuteriqi, E., Tong, A. H., van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C. (2010) The genetic landscape of a cell. Science 327, 425-431
158. Björkholm, P., and Sonnhammer, E. L. L. (2009) Comparative analysis and unification of domain-domain interaction networks. Bioinformatics 25, 3020-3025
159. Cover, T. M., and Thomas, J. A. (2006) Elements of Information Theory, 2nd Ed., Wiley-Interscience
160. Ben-Hur, A., and Noble, W. S. (2006) Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinf 7, S2
161. Alexeyenko, A., and Sonnhammer, E. L. L. (2009) Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res. 19, 1107-1116
162. van Haagen, H. H., 't Hoen, P. A., de Morrée, A., van Roon-Mom, W. M., Peters, D. J., Roos, M., Mons, B., van Ommen, G. J., and Schuemie, M. J. (2011) In silico discovery and experimental validation of new protein-protein interactions. Proteomics 11, 843-853
163. Jelier, R., Schuemie, M. J., Roes, P. J., van Mulligen, E. M., and Kors, J. A. (2008) Literature-based concept profiles for gene annotation: the issue of weighting. Int. J. Med. Inform. 77, 354-362 (Pubitemid 351434603)
164. Obayashi, T., and Kinoshita, K. (2011) COXPRESdb: a database to compare gene coexpression in seven model animals. Nucleic Acids Res. 39, D1016-1022
165. Liu, X., Yu, X., Zack, D. J., Zhu, H., and Qian, J. (2008) TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics 9, 271
166. Yellaboina, S., Tasneem, A., Zaykin, D. V., Raghavachari, B., and Jothi, R. (2011) DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Res. 39, D730-735
167. Warde-Farley, D., Donaldson, S. L., Comes, O., Zuberi, K., Badrawi, R., Chao, P., Franz, M., Grouios, C., Kazi, F., Lopes, C. T., Maitland, A., Mostafavi, S., Montojo, J., Shao, Q., Wright, G., Bader, G. D., and Morris, Q. (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 38, W214-220
168. Myers, C. L., Robson, D., Wible, A., Hibbs, M. A., Chiriac, C., Theesfeld, C. L., Dolinski, K., and Troyanskaya, O. G. (2005) Discovery of biological networks from diverse functional genomic data. Genome Biol. 6, R114
169. Kiel, C., Vogt, A., Campagna, A., Chatr-aryamontri, A., Swiatek-de Lange, M., Beer, M., Bolz, S., Mack, A. F., Kinkl, N., Cesareni, G., Serrano, L., and Ueffing, M. (2011) Structural and functional protein network analyses predict novel signaling functions for rhodopsin. Mol. Syst. Biol. 7, 551
170. Kennard, R. W., and Stone, L. A. (1969) Computer Aided Design of Experiments. Technometrics 11, 137-148