Understanding Cancer Progression Using Protein Interaction Networks

Systems Biology in Cancer Research and Drug Discovery

Volumn , Issue , 2012, Pages 167-195

  Guney, Emre ^a   Sanz Pamplona, Rebeca ^b   Sierra, Angels ^b   Oliva, Baldo ^a  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b HOSPITAL DURAN I REYNALS   (Spain)

Author keywords

Active subnetwork; Guilt by Association; Metastasis; Metastatic breast cancer; Network biology; Network medicine; Protein protein interaction

Indexed keywords

EID: 84899648381     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-94-007-4819-4_7     Document Type: Chapter

References (150)

1. Aerts S, Lambrechts D, Maity S et al (2006) Gene prioritization through genomic data fusion. Nat Biotechnol 24:537-544
2. Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK (2006) Physicochemical moDelling of cell signalling pathways. Nat Cell Biol 8:1195-1203
3. Alexeyenko A, Sonnhammer EL (2009) Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res 19:1107-1116
4. Alfarano C, AndraDe CE, Anthony K et al (2005) The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res 33:D418-D424
5. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8:450-461
6. Amberger J, Bocchini CA, Scott AF, Hamosh A (2009) McKusicks Online MenDelian Inheritance in Man (OMIM). Nucleic Acids Res 37:D793-D796
7. Apweiler R, Bairoch A, Wu CH et al (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32:D115-D119
8. Aragues R, SanDer C, Oliva B (2008) Predicting cancer involvement of genes from heterogeneous data. BMC Bioinformatics 9:172
9. Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25:25-29
10. Bairoch A, Apweiler R, Wu CH et al (2005) The universal protein resource (UniProt). Nucleic Acids Res 33:D154-D159
11. Bandyopadhyay S, Kelley R, Krogan NJ, IDeker T (2008) Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol 4:e1000065
12. Barabasi AL, Oltvai ZN (2004) Network biology: unDerstanding the cells functional organization. Nat Rev Genet 5:101-113
13. Barabasi AL, Gulbahce N, Loscalzo J (2011) Network medicine: a network-based approach to human disease. Nat Rev Genet 12:56-68
14. Barrett T, Edgar R (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 411:352-369
15. Berglund L, Bjorling E, Oksvold P et al (2008) A genecentric Human Protein Atlas for expression profiles based on antibodies. Mol Cell Proteomics 7:2019-2027
16. Berman HM, Westbrook J, Feng Z et al (2000) The protein data bank. Nucleic Acids Res 28L:235-242
17. Bhalla US (2003) UnDerstanding complex signaling networks through moDels and metaphors. Prog Biophys Mol Biol 81:45-65
18. Bhalla US, Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283:381-387
19. Bonifaci N, Berenguer A, Diez J et al (2008) Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes. BMC Med Genomics 1:62
20. Buetow KH, Klausner RD,fine H et al (2002) Cancer molecular analysis project: weaving a rich cancer research tapestry. Cancer Cell 1:315-318
21. Chen J, Aronow BJ, Jegga AG (2009) Disease candidate gene iDentification and prioritization using protein interaction networks. BMC Bioinformatics 10:73
22. Chen L, Xuan J, Riggins RB et al (2011) IDentifying cancer biomarkers by network-constrained support vector machines. BMC Syst Biol 5:161
23. Chowdhury SA, Nibbe RK, Chance MR, Koyuturk M (2011) Subnetwork state functions Define dysregulated subnetworks in cancer. J Comput Biol 18:263-281
24. Chu LH, Chen BS (2008) Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug target. BMC Syst Biol 2:56
25. Chuang HY, Lee E, Liu YT et al (2007) Network-based classification of breast cancer metastasis. Mol Syst Biol 3:140
26. Chuang HY, Hofree M, IDeker T (2010) A DecaDe of systems biology. Annu Rev Cell Dev Biol 26:721-744
27. Collins FS, Barker AD (2007) Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. Sci Am 296:50-57
28. Comen E, Norton L, Massague J (2011) Clinical implications of cancer self-seeding. Nat Rev Clin Oncol 8:369-377
29. Croft D, OKelly G, Wu G et al (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39:D691-D697
30. Csermely P, Agoston V, Pongor S (2005) The efficiency of multi-Target drugs: the network approach might help drug Design. Trends Pharmacol Sci 26:178-182
31. Dezso Z, Nikolsky Y, Nikolskaya T et al (2009) IDentifying disease-specific genes based on their topological significance in protein networks. BMC Syst Biol 3:36
32. Dickson D (1999) Wellcome funds cancer database. Nature 401:729
33. Dreze M, Monachello D, Lurin C et al (2010) High-quality binary interactome mapping. Methods Enzymol 470:281-315
34. Dutkowski J, IDeker T (2011) Protein networks as logic functions in Development and cancer. PLoS Comput Biol 7:e1002180
35. Efroni S, Schaefer CF, Buetow KH (2007) IDentification of key processes unDerlying cancer phenotypes using biologic pathway analysis. PLoS One 2:e425
36. Ergun A, Lawrence CA, Kohanski MA et al (2007) A network biology approach to prostate cancer. Mol Syst Biol 3:82
37. Ferlay J, Parkin DM, Steliarova-Foucher E (2010) Estimates of cancer inciDence and mortality in Europe in 2008. Eur J Cancer 46:765-781
38. fidler IJ (2003) The pathogenesis of cancer metastasis: the seed and soil hypothesis revisited. Nat Rev Cancer 3:453-458
39. Fliri AF, Loging WT, Volkmann RA (2010) Cause-effect relationships in medicine: a protein network perspective. Trends Pharmacol Sci 31:547-555
40. Fry DC, Vassilev LT (2005) Targeting protein-protein interactions for cancer therapy. J Mol Med (Berl) 83:955-963
41. Furney SJ, Higgins DG, Ouzounis CA, Lopez-Bigas N (2006) Structural and functional properties of genes involved in human cancer. BMC Genomics 7:3
42. Furney SJ, Calvo B, Larranaga P et al (2008) Prioritization of candidate cancer genes-An aid to oncogenomic studies. Nucleic Acids Res 36:e115
43. Futreal PA, Coin L, Marshall M et al (2004) A census of human cancer genes. Nat Rev Cancer 4:177-183
44. Garcia-Garcia J, Guney E, Aragues R et al (2010) Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics 11:56
45. Gluck S (2007) The prevention and management of distant metastases in women with breast cancer. Cancer Invest 25:6-13
46. Goh KI, Cusick ME, Valle D et al (2007) The human disease network. Proc Natl Acad Sci USA 104:8685-8690
47. Grimaldi D, Claessens YE, Mira JP, Chiche JD (2009) Beyond clinical phenotype: the biologic integratome. Crit Care Med 37:S38-S49
48. GulDener U, Munsterkotter M, Oesterheld M et al (2006) MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res 34:436-441
49. GunDem G, Perez-Llamas C, Jene-Sanz A et al (2010) IntOGen: integration and data mining of multidimensional oncogenomic data. Nat Methods 7:92-93
50. Guney E, Oliva B (2011) Toward PWAS: discovering pathways associated with human disorDers. BMC Bioinformatics 12:A12
51. Guo Z, Wang L, Li Y et al (2007) Edge-based scoring and searching method for iDentifying condition-responsive protein-protein interaction subnetwork. Bioinformatics 23:2121-2128
52. Gupta GP, Massague J (2006) Cancer metastasis: building a framework. Cell 127:679-695
53. Hamosh A, Scott AF, Amberger JS et al (2005) Online MenDelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorDers. Nucleic Acids Res 33:D514-D517
54. Han K, Park B, Kim H et al (2004) HPID: the Human Protein Interaction Database. Bioinformatics 20:2466-2470
55. Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144:646-674
56. Harris MA, Clark J, Ireland A et al (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258-D261
57. Hopkins AL (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4:682-690
58. Hortobagyi GN (2000) Developments in chemotherapy of breast cancer. Cancer 88:3073-3079
59. Hudson TJ, AnDerson W, Artez A et al (2010) International network of cancer genome projects. Nature 464:993-998
60. IDeker T, Sharan R (2008) Protein networks in disease. Genome Res 18:644-652
61. IDeker T, Ozier O, Schwikowski B, Siegel AF (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18(Suppl 1):S233-S240
62. Jonsson PF, Bates PA (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22:2291-2297
63. Joyce AR, Palsson BO (2006) The moDel organism as a system: integrating omics data sets. Nat Rev Mol Cell Biol 7:198-210
64. Justman QA, Serber Z, Ferrell JE Jr et al (2009) Tuning the activation threshold of a kinase network by nested feedback loops. Science 324:509-512
65. Kaal EC, Niel CG, Vecht CJ (2005) Therapeutic management of brain metastasis. Lancet Neurol 4:289-298
66. Kanehisa M, Goto S, Sato Y et al (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40:D109-D114
67. Kang Y, Siegel PM, Shu W et al (2003) A multigenic program mediating breast cancer metastasis to bone. Cancer Cell 3:537-549
68. Kapushesky M, Emam I, Holloway E et al (2010) Gene expression atlas at the European bioinformatics institute. Nucleic Acids Res 38:D690-D698
69. Kar G, Gursoy A, Keskin O (2009) Human cancer protein-protein interaction network: a structural perspective. PLoS Comput Biol 5:e1000601
70. Kerrien S, Aranda B, Breuza L et al (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res 40:D841-D846
71. Keshava Prasad TS, Goel R, Kandasamy K et al (2009) Human protein reference database-2009 update. Nucleic Acids Res 37:D767-D772
72. Korcsmaros T, Kovacs IA, Szalay MS, Csermely P (2007) Molecular chaperones: the modular evolution of cellular networks. J Biosci 32:441-446
73. Lage K, Karlberg EO, Storling ZM et al (2007) A human phenome-interactome network of protein complexes implicated in genetic disorDers. Nat Biotechnol 25:309-316
74. Lapointe J, Li C, Higgins JP et al (2004) Gene expression profiling iDentifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci USA 101:811-816
75. Laubenbacher R, Hower V, Jarrah A et al (2009) A systems biology view of cancer. Biochim Biophys Acta 1796:129-139
76. Lee E, Jung H, Radivojac P et al (2009) Analysis of AML genes in dysregulated molecular networks. BMC Bioinformatics 10((Suppl 9)):S2
77. Li LC, Zhao H, Shiina H et al (2003) PGDB: a curated and integrated database of genes related to the prostate. Nucleic Acids Res 31:291-293
78. Licata L, Briganti L, Peluso D et al (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40:D857-D861
79. Lim WK, Lyashenko E, Califano A (2009) Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput 2009:504-515
80. Lu X, Kang Y (2007) Organotropism of breast cancer metastasis. J Mammary Gland Biol Neoplasia 12:153-162
81. Ludwig JA, Weinstein JN (2005) Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 5:845-856
82. Luo J, Emanuele MJ, Li D et al (2009) A genome-wiDe RNAi screen iDentifies multiple synthetic lethal interactions with the Ras oncogene. Cell 137:835-848
83. Ma X, Lee H, Wang L, Sun F (2007) CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. Bioinformatics 23:215-221
84. Maayan A, Jenkins SL, Neves S et al (2005) Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science 309:1078-1083
85. Mani KM, Lefebvre C, Wang K et al (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol 4:169
86. Manning BD, Cantley LC (2007) AKT/PKB signaling: navigating downstream. Cell 129:1261-1274
87. Martin B, Aragues R, Sanz-Pamplona R et al (2008) Biological pathways contributing to organspecific phenotype of brain metastatic cells. J Proteome Res 7:908-920
88. McKusick VA (2007) MenDelian inheritance in man and its online version, OMIM. Am J Hum Genet 80:588-604
89. Michod D, Widmann C (2007) DNA-damage sensitizers: potential new therapeutical tools to improve chemotherapy. Crit Rev Oncol Hematol 63:160-171
90. Milenkovic T, Memisevic V, Ganesan AK, Przul N (2010) Systems-level cancer gene iDentification from protein interaction network topology applied to melanogenesis-related functional genomics data. J R Soc Interface 7:423-437
91. Minn AJ, Gupta GP, Siegel PM et al (2005) Genes that mediate breast cancer metastasis to lung. Nature 436:518-524
92. MulDer NJ, Apweiler R, Attwood TK et al (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 31:315-318
93. Navlakha S, Kingsford C (2010) The power of protein interaction networks for associating genes with diseases. Bioinformatics 26:1057-1063
94. Nguyen DX, Massague J (2007) Genetic Determinants of cancer metastasis. Nat Rev Genet 8:341-352
95. Nibbe RK, Markowitz S, Myeroff L et al (2009) Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer. Mol Cell Proteomics 8:827-845
96. Nibbe RK, Koyuturk M, Chance MR (2010) An integrative-omics approach to iDentify functional subnetworks in human colorectal cancer. PLoS Comput Biol 6:e1000639
97. Nibbe RK, Chowdhury SA, Koyuturk M et al (2011) Protein-protein interaction networks and subnetworks in the biology of disease. Wiley Interdiscip Rev Syst Biol Med 3:357-367
98. Nitsch D, Goncalves JP, Ojeda F et al (2010) Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics 11:460
99. Ogmen U, Keskin O, Aytuna AS et al (2005) PRISM: protein interactions by structural matching. Nucleic Acids Res 33:W331-W336
100. Ostlund G, Lindskog M, Sonnhammer EL (2010) Network-based IDentification of novel cancer genes. Mol Cell Proteomics 9:648-655
101. Paget S (1889) The distribution of secondary growths in cancer of the breast. Cancer Metastasis Rev 8:98-101
102. Palotai R, Szalay MS, Csermely P (2008) Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases. IUBMB Life 60:10-18
103. Parkinson H, Sarkans U, Kolesnikov N et al (2011) ArrayExpress update-An archive of microarray and high-Throughput sequencing-based functional genomics experiments. Nucleic Acids Res 39:D1002-D1004
104. Peri S, Navarro JD, Kristiansen TZ et al (2004) Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 32:D497-D501
105. Pujana MA, Han JD, Starita LM et al (2007) Network moDeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 39:1338-1349
106. Pujol A, Mosca R, Farres J, Aloy P (2010) Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci 31:115-123
107. Qiu YQ, Zhang S, Zhang XS, Chen L (2010) Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics 11:26
108. Quackenbush J (2006) Microarray analysis and tumor classification. N Engl J Med 354:2463-2472
109. RhoDes DR, Chinnaiyan AM (2005) Integrative analysis of the cancer transcriptome. Nat Genet 37(Suppl):S31-S37
110. RhoDes DR, Tomlin SA, Varambally S et al (2005) Probabilistic moDel of the human proteinprotein interaction network. Nat Biotechnol 23:951-959
111. RhoDes DR, Kalyana-Sundaram S, Mahavisno V et al (2007) Oncomine 3.0: genes, pathways, and networks in a collection of 18, 000 cancer gene expression profiles. Neoplasia 9:166-180
112. Russell RB, Aloy P (2008) Targeting and tinkering with interaction networks. Nat Chem Biol 4:666-673
113. Salwinski L, Miller CS, Smith AJ et al (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32:D449-D451
114. Sanz-Pamplona R, Aragues R, Stresing V et al (2007) Functional pathways shared by liver and lung metastases: a mitochondrial chaperone machine is up-regulated in soft-Tissue breast cancer metastasis. Clin Exp Metastasis 24:673-683
115. Sanz-Pamplona R, Aragues R, Driouch K et al (2011) Expression of endoplasmic reticulum stress proteins is a candidate marker of brain metastasis in both ErbB-2+ and ErbB-2-primary breast tumors. Am J Pathol 179:564-579
116. Sawyers CL (2008) The cancer biomarker problem. Nature 452:548-552
117. Schaefer CF (2004) Pathway databases. Ann N Y Acad Sci 1020:77-91
118. Schlabach MR, Luo J, Solimini NL et al (2008) Cancer proliferation gene discovery through functional genomics. Science 319:620-624
119. Scholl C, Frohling S, Dunn IF et al (2009) Synthetic lethal interaction between oncogenic KRAS DepenDency and STK33 suppression in human cancer cells. Cell 137:821-834
120. Schwartz AS, Yu J, GarDenour KR et al (2009) Cost-effective strategies for completing the interactome. Nat Methods 6:55-61
121. Schwikowski B, Uetz P,fields S (2000) A network of protein-protein interactions in yeast. Nat Biotechnol 18:1257-1261
122. Segal E, Friedman N, Koller D, Regev A (2004) A module map showing conditional activity of expression modules in cancer. Nat Genet 36:1090-1098
123. ShedDen K, Taylo JM, Enkemann SA et al (2008) Gene expression-based survival prediction in lung aDenocarcinoma: a multi-site, blinDed validation study. Nat Med 14:822-827
124. Stark C, Breitkreutz BJ, Chatr-Aryamontri A et al (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39:D698-D704
125. Steeg PS (2006) Tumor metastasis: mechanistic insights and clinical challenges. Nat Med 12:895-904
126. Strausberg RL, Simpson AJ, Wooster R (2003) Sequence-based cancer genomics: progress, lessons and opportunities. Nat Rev Genet 4:409-418
127. Su AI, Wiltshire T, Batalov S et al (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062-6067
128. Subramanian A, Tamayo P, Mootha VK et al (2005) Gene set enrichment analysis: a knowledgebased approach for interpreting genome-wiDe expression profiles. Proc Natl Acad Sci USA 102:15545-15550
129. Taylor IW, Linding R, WarDe-Farley D et al (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 27:199-204
130. The-Uniprot-Consortium (2011) Ongoing and future Developments at the Universal Protein Resource. Nucleic Acids Res 39:D214-D219
131. Tomlins SA, Mehra R, RhoDes DR et al (2007) Integrative molecular concept moDeling of prostate cancer progression. Nat Genet 39:41-51
132. Ulitsky I, Shamir R (2007) IDentification of functional modules using network topology and highthroughput data. BMC Syst Biol 1:8
133. Ulitsky I, Shamir R (2009) IDentifying functional modules using expression profiles and confiDencescored protein interactions. Bioinformatics 25:1158-1164
134. Ulitsky I, Shlomi T, Kupiec M, Shamir R (2008) From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol 4:209
135. Valastyan S, Weinberg RA (2011) Tumor metastasis: molecular insights and evolving paradigms. Cell 147:275-292
136. van De Vijver MJ, He YD, vant Veer LJ et al (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347:1999-2009
137. Vanunu O, Magger O, Ruppin E et al (2010) Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol 6:e1000641
138. Vazquez A (2009) Optimal drug combinations and minimal hitting sets. BMC Syst Biol 3:81
139. Venkatesan K, Rual JF, Vazquez A et al (2009) An empirical framework for binary interactome mapping. Nat Methods 6:83-90
140. Vidal M, Cusick ME, Barabasi AL (2011) Interactome networks and human disease. Cell 144:986-998
141. Vogelstein B, Kinzle KW (2004) Cancer genes and the pathways they control. Nat Med 10:789-799
142. Von Mering C, Huynen M, Jaeggi D et al (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 31:258-261
143. 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
144. Waltregny D, Bellahcene A, De Leval X et al (2000) Increased expression of bone sialoprotein in bone metastases compared with visceral metastases in human breast and prostate cancers. J Bone Miner Res 15:34-843
145. Wang Y, Klijn JG, Zhang Y et al (2005) Gene-expression profiles to predict distant metastasis of lymph-noDe-negative primary breast cancer. Lancet 365:671-679
146. Weigelt B, Mackay A, AHern R et al (2010) Breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol 11:339-349
147. Weng G, Bhalla US, Iyengar R (1999) Complexity in biological signaling systems. Science 284:92-96
148. Wood LD, Parsons DW, Jones S et al (2007) The genomic landscapes of human breast and colorectal cancers. Science 318:1108-1113
149. Wu X, Jiang R, Zhang MQ, LI S (2008) Network-based global inference of human disease genes. Mol Syst Biol 4:189
150. Yang K, Bai H, Ouyang Q et al (2008)finding multiple target optimal intervention in diseaserelated molecular network. Mol Syst Biol 4:228