Network-based pipeline for analyzing MS data: An application toward liver cancer

Journal of Proteome Research

Volumn 10, Issue 5, 2011, Pages 2261-2272

  Goh, Wilson Wen Bin ^a,b   Lee, Yie Hou ^c   Zubaidah, Ramdzan M ^d   Jin, Jingjing ^b   Dong, Difeng ^b   Lin, Qingsong ^b   Chung, Maxey C M ^b,e   Wong, Limsoon ^b,e  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c SINGAPORE MIT ALLIANCE FOR RESEARCH AND TECHNOLOGY   (Singapore)

^d MCGILL UNIVERSITY   (Canada)

^e NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

bioinformatics; HCC (hepatocellular carcinoma); liver cancer; protein networks; proteomics; systems biology

Indexed keywords

CYCLINE; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE 1; PROTEIN; PROTEIN PRKDC; PROTEIN XRCC5; PROTEIN XRCC6; PROTEOME; UNCLASSIFIED DRUG; WERNER SYNDROME PROTEIN;

ADVANCED CANCER; ARTICLE; BIOINFORMATICS; CANCER GROWTH; CLINICAL ARTICLE; HUMAN; HUMAN TISSUE; LIVER CELL CARCINOMA; MALE; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS;

CARCINOMA, HEPATOCELLULAR; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LIVER NEOPLASMS; MALE; PEPTIDES; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 79955797347     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr1010845     Document Type: Article

References (49)

1. Cox, J.; Mann, M. Is proteomics the new genomics? Cell 2007, 130 (3) 395-8 (Pubitemid 47198310)
2. Mann, M.; Kelleher, N. L. Precision proteomics: the case for high resolution and high mass accuracy Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (47) 18132-8
3. Hanash, S.; Taguchi, A. The grand challenge to decipher the cancer proteome Nat. Rev. Cancer 2010, 10 (9) 652-60
4. El-Serag, H. B. Hepatocellular carcinoma: recent trends in the United States Gastroenterology 2004, 127 (5 Suppl 1) S27-34
5. Villanueva, A.; Minguez, B.; Forner, A.; Reig, M.; Llovet, J. M. Hepatocellular carcinoma: novel molecular approaches for diagnosis, prognosis, and therapy Annu. Rev. Med. 2010, 61, 317-28
6. Ralhan, R.; Desouza, L. V.; Matta, A.; Chandra Tripathi, S.; Ghanny, S.; Datta Gupta, S.; Bahadur, S.; Siu, K. W. Discovery and verification of head-and-neck cancer biomarkers by differential protein expression analysis using iTRAQ labeling, multidimensional liquid chromatography, and tandem mass spectrometry Mol. Cell. Proteomics 2008, 7 (6) 1162-73 (Pubitemid 351943962)
7. Sutton, C. W.; Rustogi, N.; Gurkan, C.; Scally, A.; Loizidou, M. A.; Hadjisavvas, A.; Kyriacou, K. Quantitative proteomic profiling of matched normal and tumor breast tissues J. Proteome Res. 2010, 9 (8) 3891-902
8. Gan, C. S.; Chong, P. K.; Pham, T. K.; Wright, P. C. Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ) J. Proteome Res. 2007, 6 (2) 821-7 (Pubitemid 46340185)
9. Gramolini, A. O.; Kislinger, T.; Alikhani-Koopaei, R.; Fong, V.; Thompson, N. J.; Isserlin, R.; Sharma, P.; Oudit, G. Y.; Trivieri, M. G.; Fagan, A.; Kannan, A.; Higgins, D. G.; Huedig, H.; Hess, G.; Arab, S.; Seidman, J. G.; Seidman, C. E.; Frey, B.; Perry, M.; Backx, P. H.; Liu, P. P.; MacLennan, D. H.; Emili, A. Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses Mol. Cell. Proteomics 2008, 7 (3) 519-33 (Pubitemid 351472462)
10. Ramakrishnan, S. R.; Vogel, C.; Kwon, T.; Penalva, L. O.; Marcotte, E. M.; Miranker, D. P. Mining gene functional networks to improve mass-spectrometry-based protein identification Bioinformatics 2009, 25 (22) 2955-61
11. Sivachenko, A. Y.; Yuryev, A.; Daraselia, N.; Mazo, I. Molecular networks in microarray analysis J. Bioinform. Comput. Biol. 2007, 5 (2B) 429-56
12. Chua, H. N.; Sung, W. K.; Wong, L. Using indirect protein interactions for the prediction of Gene Ontology functions BMC Bioinform. 2007, 8 (Suppl 4) S8
13. Chua, H. N.; Ning, K.; Sung, W. K.; Leong, H. W.; Wong, L. Using indirect protein-protein interactions for protein complex predication Comput. Syst. Bioinform. Conf. 2007, 6, 97-109
14. Liu, G.; Wong, L.; Chua, H. N. Complex discovery from weighted PPI networks Bioinformatics 2009, 25 (15) 1891-7
15. Palla, G.; Derenyi, I.; Farkas, I.; Vicsek, T. Uncovering the overlapping community structure of complex networks in nature and society Nature 2005, 435 (7043) 814-8 (Pubitemid 40839731)
16. Newman, M. E.; Girvan, M. Finding and evaluating community structure in networks Phys. Rev. E: Stat. Nonlin. Soft Matter Phys. 2004, 69 (2 Pt 2) 026113
17. Bader, G. D.; Hogue, C. W. An automated method for finding molecular complexes in large protein interaction networks BMC Bioinform. 2003, 4, 2
18. Enright, A. J.; Van Dongen, S.; Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families Nucleic Acids Res. 2002, 30 (7) 1575-84 (Pubitemid 34679732)
19. Soh, D.; Dong, D.; Guo, Y.; Wong, L. Consistency, comprehensiveness, and compatibility of pathway databases BMC Bioinform. 2010, 11, 449
20. Liang, C. R.; Leow, C. K.; Neo, J. C.; Tan, G. S.; Lo, S. L.; Lim, J. W.; Seow, T. K.; Lai, P. B.; Chung, M. C. Proteome analysis of human hepatocellular carcinoma tissues by two-dimensional difference gel electrophoresis and mass spectrometry Proteomics 2005, 5 (8) 2258-71 (Pubitemid 40770587)
21. Zubaidah, R. M.; Tan, G. S.; Tan, S. B.; Lim, S. G.; Lin, Q.; Chung, M. C. 2-D DIGE profiling of hepatocellular carcinoma tissues identified isoforms of far upstream binding protein (FUBP) as novel candidates in liver carcinogenesis Proteomics 2008, 8 (23-24) 5086-96
22. Zubaidah, R. M. A comprehensive proteome analysis of hepatitis B virus- associated hepatocellular carcinoma; National University of Singapore, 2009.
23. Tan, H. T.; Tan, S.; Lin, Q.; Lim, T. K.; Hew, C. L.; Chung, M. C. Quantitative and temporal proteome analysis of butyrate-treated colorectal cancer cells Mol. Cell. Proteomics 2008, 7 (6) 1174-85 (Pubitemid 351943963)
24. Prasad, T. S.; Kandasamy, K.; Pandey, A. Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology Methods Mol. Biol. 2009, 577, 67-79
25. Stark, C.; Breitkreutz, B. J.; Reguly, T.; Boucher, L.; Breitkreutz, A.; Tyers, M. BioGRID: a general repository for interaction datasets Nucleic Acids Res. 2006, 34 (Database issue) D535-9
26. Aranda, B.; Achuthan, P.; Alam-Faruque, Y.; Armean, I.; Bridge, A.; Derow, C.; Feuermann, M.; Ghanbarian, A. T.; Kerrien, S.; Khadake, J.; Kerssemakers, J.; Leroy, C.; Menden, M.; Michaut, M.; Montecchi-Palazzi, L.; Neuhauser, S. N.; Orchard, S.; Perreau, V.; Roechert, B.; van Eijk, K.; Hermjakob, H. The IntAct molecular interaction database in 2010 Nucleic Acids Res. 2010, 38 (Database issue) D525-31
27. Hermjakob, H.; Montecchi-Palazzi, L.; Lewington, C.; Mudali, S.; Kerrien, S.; Orchard, S.; Vingron, M.; Roechert, B.; Roepstorff, P.; Valencia, A.; Margalit, H.; Armstrong, J.; Bairoch, A.; Cesareni, G.; Sherman, D.; Apweiler, R. IntAct: an open source molecular interaction database Nucleic Acids Res. 2004, 32 (Database issue) D452-5
28. Xenarios, I.; Salwinski, L.; Duan, X. J.; Higney, P.; Kim, S. M.; Eisenberg, D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions Nucleic Acids Res. 2002, 30 (1) 303-5 (Pubitemid 34679570)
29. Xenarios, I.; Fernandez, E.; Salwinski, L.; Duan, X. J.; Thompson, M. J.; Marcotte, E. M.; Eisenberg, D. DIP: The Database of Interacting Proteins: 2001 update Nucleic Acids Res. 2001, 29 (1) 239-41 (Pubitemid 32054458)
30. Xenarios, I.; Rice, D. W.; Salwinski, L.; Baron, M. K.; Marcotte, E. M.; Eisenberg, D. DIP: the database of interacting proteins Nucleic Acids Res. 2000, 28 (1) 289-91 (Pubitemid 30047782)
31. Rual, J. F.; Venkatesan, K.; Hao, T.; Hirozane-Kishikawa, T.; Dricot, A.; Li, N.; Berriz, G. F.; Gibbons, F. D.; Dreze, M.; Ayivi-Guedehoussou, N.; Klitgord, N.; Simon, C.; Boxem, M.; Milstein, S.; Rosenberg, J.; Goldberg, D. S.; Zhang, L. V.; Wong, S. L.; Franklin, G.; Li, S.; Albala, J. S.; Lim, J.; Fraughton, C.; Llamosas, E.; Cevik, S.; Bex, C.; Lamesch, P.; Sikorski, R. S.; Vandenhaute, J.; Zoghbi, H. Y.; Smolyar, A.; Bosak, S.; Sequerra, R.; Doucette-Stamm, L.; Cusick, M. E.; Hill, D. E.; Roth, F. P.; Vidal, M. Towards a proteome-scale map of the human protein-protein interaction network Nature 2005, 437 (7062) 1173-8 (Pubitemid 41509356)
32. Stelzl, U.; Worm, U.; Lalowski, M.; Haenig, C.; Brembeck, F. H.; Goehler, H.; Stroedicke, M.; Zenkner, M.; Schoenherr, A.; Koeppen, S.; Timm, J.; Mintzlaff, S.; Abraham, C.; Bock, N.; Kietzmann, S.; Goedde, A.; Toksoz, E.; Droege, A.; Krobitsch, S.; Korn, B.; Birchmeier, W.; Lehrach, H.; Wanker, E. E. A human protein-protein interaction network: a resource for annotating the proteome Cell 2005, 122 (6) 957-68 (Pubitemid 41345212)
33. Kanehisa, M. Representation and analysis of molecular networks involving diseases and drugs Genome Inform. 2009, 23 (1) 212-3
34. Kelder, T.; Pico, A. R.; Hanspers, K.; van Iersel, M. P.; Evelo, C.; Conklin, B. R. Mining biological pathways using WikiPathways web services PLoS One 2009, 4 (7) e6447
35. Pico, A. R.; Kelder, T.; van Iersel, M. P.; Hanspers, K.; Conklin, B. R.; Evelo, C. WikiPathways: pathway editing for the people PLoS Biol. 2008, 6 (7) e184
36. Jimenez-Marin, A.; Collado-Romero, M.; Ramirez-Boo, M.; Arce, C.; Garrido, J. J. Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis BMC Proc. 2009, 3 (Suppl 4) S6
37. Floyd, R. W. Algorithm 97: Shortest Path Commun. ACM 1962, 5 (6) 345
38. Searle, B. C.; Turner, M.; Nesvizhskii, A. I. Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies J. Proteome Res. 2008, 7 (1) 245-53 (Pubitemid 351171137)
39. Nesvizhskii, A. I.; Roos, F. F.; Grossmann, J.; Vogelzang, M.; Eddes, J. S.; Gruissem, W.; Baginsky, S.; Aebersold, R. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides Mol. Cell. Proteomics 2006, 5 (4) 652-70
40. Mathivanan, S.; Periaswamy, B.; Gandhi, T. K.; Kandasamy, K.; Suresh, S.; Mohmood, R.; Ramachandra, Y. L.; Pandey, A. An evaluation of human protein-protein interaction data in the public domain BMC Bioinform. 2006, 7 (Suppl 5) S19
41. Kato, K.; Yamashita, R.; Matoba, R.; Monden, M.; Noguchi, S.; Takagi, T.; Nakai, K. Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues Nucleic Acids Res. 2005, 33 (Database issue) D533-6
42. Washburn, M. P.; Wolters, D.; Yates, J. R., 3rd Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 2001, 19 (3) 242-7 (Pubitemid 32220565)
43. Yang, X.; Lazar, I. M. MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides BMC Cancer 2009, 9, 96
44. Donato, F.; Tagger, A.; Gelatti, U.; Parrinello, G.; Boffetta, P.; Albertini, A.; Decarli, A.; Trevisi, P.; Ribero, M. L.; Martelli, C.; Porru, S.; Nardi, G. Alcohol and hepatocellular carcinoma: the effect of lifetime intake and hepatitis virus infections in men and women Am. J. Epidemiol. 2002, 155 (4) 323-31 (Pubitemid 34132050)
45. Pachiadakis, I.; Pollara, G.; Chain, B. M.; Naoumov, N. V. Is hepatitis C virus infection of dendritic cells a mechanism facilitating viral persistence? Lancet Infect. Dis. 2005, 5 (5) 296-304 (Pubitemid 40602249)
46. Melen, K.; Fagerlund, R.; Nyqvist, M.; Keskinen, P.; Julkunen, I. Expression of hepatitis C virus core protein inhibits interferon-induced nuclear import of STATs J. Med. Virol. 2004, 73 (4) 536-47 (Pubitemid 38857203)
47. Branda, M.; Wands, J. R. Signal transduction cascades and hepatitis B and C related hepatocellular carcinoma Hepatology 2006, 43 (5) 891-902 (Pubitemid 43724611)
48. Dang, C. V.; Semenza, G. L. Oncogenic alterations of metabolism Trends Biochem. Sci. 1999, 24 (2) 68-72 (Pubitemid 29346576)
49. Wang, D.; Dubois, R. N. Eicosanoids and cancer Nat. Rev. Cancer 2010, 10 (3) 181-93