| [1] | De Las Rivas J, de Luis A (2004) Interactome data and databases: different types of protein interaction. Comp Funct Genomics 5: 173–178. doi: 10.1002/cfg.377
|
| [2] | Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101–113. doi: 10.1038/nrg1272
|
| [3] | Grindrod P, Kibble M (2004) Review of uses of network and graph theory concepts within proteomics. Expert Rev Proteomics 1: 229–238. doi: 10.1586/14789450.1.2.229
|
| [4] | Pazos F, Ranea JA, Juan D, Sternberg MJ (2005) Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J Mol Biol 352: 1002–1015. doi: 10.1016/j.jmb.2005.07.005
|
| [5] | Kann MG (2007) Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform 8: 333–346. doi: 10.1093/bib/bbm031
|
| [6] | Ideker T, Sharan R (2008) Protein networks in disease. Genome Res 18: 644–652. doi: 10.1101/gr.071852.107
|
| [7] | Huntington G (1872) On chorea. Med Surg Rep 26: 320–321.
|
| [8] | Punnett RC (1908) Mendelism in Relation to Disease. Proc R Soc Med 1: 135–168.
|
| [9] | A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group. Cell 72: 971–983. doi: 10.1016/0092-8674(93)90585-e
|
| [10] | Goehler H, Lalowski M, Stelzl U, Waelter S, Stroedicke M, et al. (2004) A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell 15: 853–865. doi: 10.1016/j.molcel.2004.09.016
|
| [11] | Duennwald ML, Jagadish S, Giorgini F, Muchowski PJ, Lindquist S (2006) A network of protein interactions determines polyglutamine toxicity. Proc Natl Acad Sci U S A 103: 11051–11056. doi: 10.1073/pnas.0604548103
|
| [12] | Giorgini F, Muchowski PJ (2005) Connecting the dots in Huntington's disease with protein interaction networks. Genome Biol 6: 210.
|
| [13] | Shoemaker BA, Panchenko AR (2007) Deciphering protein–protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol 3: e42 doi:10.1371/journal.pcbi.0030043.
|
| [14] | Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, et al. (2010) The genetic landscape of a cell. Science 327: 425–431. doi: 10.1126/science.1180823
|
| [15] | Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569–4574. doi: 10.1073/pnas.061034498
|
| [16] | Mrowka R, Patzak A, Herzel H (2001) Is there a bias in proteome research? Genome Res 11: 1971–1973. doi: 10.1101/gr.206701
|
| [17] | von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399–403. doi: 10.1038/nature750
|
| [18] | Shoemaker BA, Panchenko AR, Bryant SH (2006) Finding biologically relevant protein domain interactions: conserved binding mode analysis. Protein Sci 15: 352–361. doi: 10.1110/ps.051760806
|
| [19] | Sprinzak E, Margalit H (2001) Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 311: 681–692. doi: 10.1006/jmbi.2001.4920
|
| [20] | Deng M, Mehta S, Sun F, Chen T (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Res 12: 1540–1548. doi: 10.1101/gr.153002
|
| [21] | Nye TM, Berzuini C, Gilks WR, Babu MM, Teichmann SA (2005) Statistical analysis of domains in interacting protein pairs. Bioinformatics 21: 993–1001. doi: 10.1093/bioinformatics/bti086
|
| [22] | Fraser HB, Hirsh AE, Wall DP, Eisen MB (2004) Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A 101: 9033–9038. doi: 10.1073/pnas.0402591101
|
| [23] | Kanaan SP, Huang C, Wuchty S, Chen DZ, Izaguirre JA (2009) Inferring protein-protein interactions from multiple protein domain combinations. Methods Mol Biol 541: 43–59. doi: 10.1007/978-1-59745-243-4_3
|
| [24] | Guimaraes KS, Przytycka TM (2008) Interrogating domain-domain interactions with parsimony based approaches. BMC Bioinformatics 9: 171. doi: 10.1186/1471-2105-9-171
|
| [25] | Guimaraes KS, Jothi R, Zotenko E, Przytycka TM (2006) Predicting domain-domain interactions using a parsimony approach. Genome Biol 7: R104. doi: 10.1186/gb-2006-7-11-r104
|
| [26] | Riley R, Lee C, Sabatti C, Eisenberg D (2005) Inferring protein domain interactions from databases of interacting proteins. Genome Biol 6: R89. doi: 10.1186/gb-2005-6-10-r89
|
| [27] | Izarzugaza JM, Juan D, Pons C, Ranea JA, Valencia A, et al. (2006) TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res 34: W315–319. doi: 10.1093/nar/gkl112
|
| [28] | Gertz J, Elfond G, Shustrova A, Weisinger M, Pellegrini M, et al. (2003) Inferring protein interactions from phylogenetic distance matrices. Bioinformatics 19: 2039–2045. doi: 10.1093/bioinformatics/btg278
|
| [29] | 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. doi: 10.1006/jmbi.2000.3732
|
| [30] | Goh CS, Cohen FE (2002) Co-evolutionary analysis reveals insights into protein-protein interactions. J Mol Biol 324: 177–192. doi: 10.1016/s0022-2836(02)01038-0
|
| [31] | Jothi R, Kann MG, Przytycka TM (2005) Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics 21 Suppl 1: i241–i250. doi: 10.1093/bioinformatics/bti1009
|
| [32] | Pazos F, Helmer-Citterich M, Ausiello G, Valencia A (1997) Correlated mutations contain information about protein-protein interaction. J Mol Biol 271: 511–523. doi: 10.1006/jmbi.1997.1198
|
| [33] | Pazos F, Valencia A (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47: 219–227. doi: 10.1002/prot.10074
|
| [34] | Ramani AK, Marcotte EM (2003) Exploiting the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol 327: 273–284. doi: 10.1016/s0022-2836(03)00114-1
|
| [35] | Jothi R, Cherukuri PF, Tasneem A, Przytycka TM (2006) Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain-Domain Interactions Mediating Protein-Protein Interactions. J Mol Biol 362: 861–875. doi: 10.1016/j.jmb.2006.07.072
|
| [36] | 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 U S A 96: 4285–4288. doi: 10.1073/pnas.96.8.4285
|
| [37] | Huynen MA, Bork P (1998) Measuring genome evolution. Proc Natl Acad Sci U S A 95: 5849–5856. doi: 10.1073/pnas.95.11.5849
|
| [38] | Dandekar T, Snel B, Huynen M, Bork P (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23: 324–328. doi: 10.1016/s0968-0004(98)01274-2
|
| [39] | 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. doi: 10.1073/pnas.96.6.2896
|
| [40] | Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, et al. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751–753. doi: 10.1126/science.285.5428.751
|
| [41] | Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86–90. doi: 10.1038/47056
|
| [42] | Juan D, Pazos F, Valencia A (2008) Co-evolution and co-adaptation in protein networks. FEBS Lett doi: 10.1016/j.febslet.2008.02.017
|
| [43] | Valencia A, Pazos F (2003) Prediction of protein-protein interactions from evolutionary information. Methods Biochem Anal 44: 411–426. doi: 10.1002/0471721204.ch20
|
| [44] | Valencia A, Pazos F (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 12: 368–373. doi: 10.1016/s0959-440x(02)00333-0
|
| [45] | Pazos F, Valencia A (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 14: 609–614. doi: 10.1093/protein/14.9.609
|
| [46] | Pazos F, Juan D, Izarzugaza JM, Leon E, Valencia A (2008) Prediction of protein interaction based on similarity of phylogenetic trees. Methods Mol Biol 484: 523–535. doi: 10.1007/978-1-59745-398-1_31
|
| [47] | Fryxell KJ (1996) The coevolution of gene family trees. Trends Genet 12: 364–369. doi: 10.1016/s0168-9525(96)80020-5
|
| [48] | Hakes L, Lovell SC, Oliver SG, Robertson DL (2007) Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proc Natl Acad Sci U S A 104: 7999–8004. doi: 10.1073/pnas.0609962104
|
| [49] | Tillier ER, Charlebois RL (2009) The human protein coevolution network. Genome Res 19: 1861–1871. doi: 10.1101/gr.092452.109
|
| [50] | Sato T, Yamanishi Y, Kanehisa M, Toh H (2005) The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21: 3482–3489. doi: 10.1093/bioinformatics/bti564
|
| [51] | Kann MG, Jothi R, Cherukuri PF, Przytycka TM (2007) Predicting protein domain interactions from coevolution of conserved regions. Proteins 67: 811–820. doi: 10.1002/prot.21347
|
| [52] | Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33 Suppl: 228–237. doi: 10.1038/ng1090
|
| [53] | Kerem B, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, et al. (1989) Identification of the cystic fibrosis gene: genetic analysis. Science 245: 1073–1080. doi: 10.1126/science.2570460
|
| [54] | Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, et al. (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266: 66–71. doi: 10.1126/science.7545954
|
| [55] | Wooster R, Bignell G, Lancaster J, Swift S, Seal S, et al. (1995) Identification of the breast cancer susceptibility gene BRCA2. Nature 378: 789–792. doi: 10.1038/378789a0
|
| [56] | Scriver CR, Waters PJ (1999) Monogenic traits are not simple: lessons from phenylketonuria. Trends Genet 15: 267–272. doi: 10.1016/s0168-9525(99)01761-8
|
| [57] | Groman JD, Meyer ME, Wilmott RW, Zeitlin PL, Cutting GR (2002) Variant cystic fibrosis phenotypes in the absence of CFTR mutations. N Engl J Med 347: 401–407. doi: 10.1056/nejmoa011899
|
| [58] | Sun H, Smallwood PM, Nathans J (2000) Biochemical defects in ABCR protein variants associated with human retinopathies. Nature Genet 26: 242–246. doi: 10.1038/79994
|
| [59] | Dipple KM, McCabe ERB (2000) Phenotypes of patients with ‘simple’ Mendelian disorders are complex traits: thresholds, modifiers, and systems dynamics. Am J Hum Genet 66: 1729–1735. doi: 10.1086/302938
|
| [60] | Van Heyningen V, Yeyati PL (2004) Mechanisms of non-Mendelian inheritance in genetic disease. Hum Mol Genet 13 Spec No 2: R225–233. doi: 10.1093/hmg/ddh254
|
| [61] | Mayeux R (2005) Mapping the new frontier: complex genetic disorders. J Clin Invest 115: 1404–1407. doi: 10.1172/jci25421
|
| [62] | Brauch H, Kishida T, Glavac D, Chen F, Pausch F, et al. (1995) Von Hippel-Lindau (VHL) disease with pheochromocytoma in the Black Forest region of Germany: evidence for a founder effect. Hum Genet 95: 551–556. doi: 10.1007/bf00223868
|
| [63] | Ohh M, Park CW, Ivan M, Hoffman MA, Kim TY, et al. (2000) Ubiquitination of hypoxia-inducible factor requires direct binding to the beta-domain of the von Hippel-Lindau protein. Nat Cell Biol 2: 423–427.
|
| [64] | Association ASH (2007) HPV Resource Center.
|
| [65] | Scheffner M, Whitaker NJ (2003) Human papillomavirus-induced carcinogenesis and the ubiquitin-proteasome system. Semin Cancer Biol 13: 59–67. doi: 10.1016/s1044-579x(02)00100-1
|
| [66] | Chuang HY, Lee E, Liu YT, Lee D, Ideker T (2007) Network-based classification of breast cancer metastasis. Mol Syst Biol 3: 140. doi: 10.1038/msb4100180
|
| [67] | Ideker T, Ozier O, Schwikowski B, Siegel AF (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 Suppl 1: S233–240. doi: 10.1093/bioinformatics/18.suppl_1.s233
|
| [68] | Hallock P, Thomas MA (2012) Integrating the Alzheimer's disease proteome and transcriptome: a comprehensive network model of a complex disease. OMICS 16: 37–49. doi: 10.1089/omi.2011.0054
|
| [69] | Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173–1178. doi: 10.1038/nature04209
|
| [70] | Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database–2009 update. Nucleic Acids Res 37: D767–772. doi: 10.1093/nar/gkn892
|
| [71] | Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685–8690. doi: 10.1073/pnas.0701361104
|
| [72] | Wachi S, Yoneda K, Wu R (2005) Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics 21: 4205–4208. doi: 10.1093/bioinformatics/bti688
|
| [73] | Jonsson PF, Bates PA (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22: 2291–2297. doi: 10.1093/bioinformatics/btl390
|
| [74] | Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, et al. (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311: 239–242. doi: 10.1126/science.1116804
|
| [75] | Lim J, Hao T, Shaw C, Patel AJ, Szabo G, et al. (2006) A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125: 801–814. doi: 10.1016/j.cell.2006.03.032
|
| [76] | Charlesworth JC, Curran JE, Johnson MP, Goring HH, Dyer TD, et al. Transcriptomic epidemiology of smoking: the effect of smoking on gene expression in lymphocytes. BMC Med Genomics 3: 29. doi: 10.1186/1755-8794-3-29
|
| [77] | Oti M, Snel B, Huynen MA, Brunner HG (2006) Predicting disease genes using protein-protein interactions. J Med Genet 43: 691–698. doi: 10.1136/jmg.2006.041376
|
| [78] | Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38: 285–293. doi: 10.1038/ng1747
|
| [79] | Chen L, Tai J, Zhang L, Shang Y, Li X, et al. (2011) Global risk transformative prioritization for prostate cancer candidate genes in molecular networks. Mol Biosyst 7: 2547–2553. doi: 10.1039/c1mb05134b
|
| [80] | Xu J, Li Y (2006) Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics 22: 2800–2805. doi: 10.1093/bioinformatics/btl467
|
| [81] | Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tatar D, et al. (2011) Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet 7: e1001273 doi:10.1371/journal.pgen.1001273.
|
| [82] | Jiang Z, Zhou Y (2005) Using bioinformatics for drug target identification from the genome. Am J Pharmacogenomics 5: 387–396. doi: 10.2165/00129785-200505060-00005
|
| [83] | Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M (2007) Drug-target network. Nat Biotechnol 25: 1119–1126. doi: 10.1038/nbt1338
|
| [84] | Hall SS Revolution postponed. Sci Am 303: 60–67. doi: 10.1038/scientificamerican1010-60
|
| [85] | Nadeau JH (2009) Transgenerational genetic effects on phenotypic variation and disease risk. Hum Mol Genet 18: R202–R210. doi: 10.1093/hmg/ddp366
|
| [86] | CDC (2006) Epstein-Barr Virus and Infectious Mononucleosis. Center for Disease Control and Prevention/National Center for Infectious Diseases.
|
| [87] | Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, et al. (2007) Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A 104: 7606–7611. doi: 10.1073/pnas.0702332104
|
| [88] | Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431–432. doi: 10.1093/bioinformatics/btq675
|
| [89] | Zhang J, Yang Y, Wang Y, Wang Z, Yin M, et al. (2011) Identification of hub genes related to the recovery phase of irradiation injury by microarray and integrated gene network analysis. PLoS ONE 6: e24680 doi:10.1371/journal.pone.0024680.
|
