A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression

International Journal of Bioinformatics Research and Applications

Volumn 8, Issue 3-4, 2012, Pages 155-170

  Goh, Wilson Wen Bin ^a   Lee, Yie Hou ^b   Ramdzan, Zubaidah M ^c   Chung, Maxey C M ^d   Wong, Limsoon ^d   Sergot, Marek J ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

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

^c MCGILL UNIVERSITY   (Canada)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Biological networks; HCC; Hepatitis B; Liver cancer; Maxlink; PPINs; Proteomics expansion pipeline

Indexed keywords

EID: 84866238951     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2012.048967     Document Type: Article

References (37)

1. Adamcsek, B., Palla, G., Farkas, I.J., Derényi, I. and Vicsek, T. (2006) 'Cfinder: locating cliques and overlapping modules in biological networks', Bioinformatics, Vol. 22, No. 8, April, pp.1021-1023.
2. Alexeyenko, A. and Sonnhammer, E.L.L. (2009) 'Global networks of functional coupling in eukaryotes from comprehensive data integration', Genome Res., Vol. 19, No. 6, June, pp.1107-1116.
3. 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. and Hermjakob, H. (2010) 'The intact molecular interaction database in 2010', Nucleic Acids Res., Vol. 38, Database issue, January, D525-D531.
4. Buchanan, F.G., Gorden, D.L., Matta, P., Shi, Q., Matrisian, L.M. and DuBois, R.N. (2006) 'Role of beta-arrestin 1 in the metastatic progression of colorectal cancer', Proc. Natl. Acad. Sci. USA, Vol. 103, No. 5, January, pp.1492-1497. (Pubitemid 43191193)
5. Chang, T.J., Juan, C.C., Yin, P.H., Chi, C.W. and Tsay, H.J. (1998) 'Up-regulation of betaactin, cyclophilin and gapdh in n1s1 rat hepatoma', Oncol. Rep., Vol. 5, No. 2, pp.469-471.
6. Chen, J. and Yuan, B. (2006) 'Detecting functional modules in the yeast proteinprotein interaction network', Bioinformatics, Vol. 22, No. 18, September, pp.2283-2290. (Pubitemid 44390885)
7. Cheok, M.H., Yang, W., Pui, C-H., Downing, J.R., Cheng, C., Naeve, C.W., Relling, M.V. and Evans, W.E. (2003) 'Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells', Nat. Genet, Vol. 34, No. 1, May, 85-90. (Pubitemid 36548796)
8. Choe, L., D'Ascenzo, M., Relkin, N.R., Pappin, D., Ross, P., Williamson, B., Guertin, S., Pribil, P. and Lee, K.H. (2007) '8-plex quantitation of changes in cerebrospinal uid protein expression in subjects undergoing intravenous immunoglobulin treatment for alzheimer's disease', Proteomics, Vol. 7, No. 20, October, pp.3651-3660. (Pubitemid 350022271)
9. El-Serag, H.B. (2004) 'Hepatocellular carcinoma: recent trends in the united states', Gastroenterology, Vol. 127, 5 Suppl 1, November, pp.S27-S34. (Pubitemid 39423367)
10. Fukui, K., Tamura, S., Wada, A., Kamada, Y., Sawai, Y., Imanaka, K., Kudara, T., Shimomura, I. and Hayashi, N. (2006) 'Expression and prognostic role of rhoa gtpases in hepatocellular carcinoma', J. Cancer Res. Clin. Oncol., Vol. 132, No. 10, October, pp.627-633. (Pubitemid 44310328)
11. Futreal, P.A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N. and Stratton, M.R. (2004) 'A. census of human cancer genes', Nat. Rev. Cancer, Vol. 4, No. 3, March, pp.177-183.
12. Goh, W.W.B., Lee, Y.H., Ramdzan, Z.M., Chung, M.C.M., Wong, L. and Sergot, M.J. (xxxx) 'A networkbased maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression', Int. J. Bioinformatics Research and Applications, Vol. x, No. x, pp.xxx-xxx.
13. Goidin, D., Mamessier, A., Staquet, M.J., Schmitt, D. and Berthier-Vergnes, O. (2001) 'Ribosomal 18s rna prevails over glyceraldehyde-3-phosphate dehydrogenase and beta-actin genes as internal standard for quantitative comparison of mrna levels in invasive and noninvasive human melanoma cell subpopulations', Anal. Biochem, Vol. 295, No. 1, August, pp.17-21. (Pubitemid 32721736)
14. Hishigaki, H., Nakai, K., Ono, T., Tanigami, A. and Takagi, T. (2001) 'Assessment of prediction accuracy of protein function from protein-protein interaction data', Yeast, Vol. 18, No. 6, April, 523-531.
15. Liu, G., Wong, L. and Chua, H.N. (2009) 'Complex discovery from weighted ppi networks', Bioinformatics, Vol. 25, No. 15, August, pp.1891-1897.
16. rd. (2004) 'A model for random sampling and estimation of relative protein abundance in shotgun proteomics', Anal. Chem, Vol. 76, No. 14, July, pp.4193-4201. (Pubitemid 38943698)
17. Lupberger, J., Kreuzer, K.A., Baskaynak, G., Peters, U.R., le Coutre, P. and Schmidt, C.A. (2002) 'Quantitative analysis of beta-actin, beta-2-microglobulin and porphobilinogen deaminase mrna and their comparison as control transcripts for rt-pcr', Mol. Cell Probes, Vol. 16, No. 1, February, pp.25-30. (Pubitemid 34246207)
18. Moon, E-J., Jeong, C-H., Jeong, J-W., Kim, K.R., Yu, D-Y., Murakami, S., Kim, C.W. and Kim, K-W. (2004) 'Hepatitis b virus x protein induces angiogenesis by stabilizing hypoxia-inducible factor-1alpha', FASEB J., Vol. 18, No. 2, February, pp.382-384.
19. Moore, M.J. (2005) 'From birth to death: the complex lives of eukaryotic mrnas', Science, Vol. 309, No. 5740, September, pp.1514-1518. (Pubitemid 41266467)
20. Nowak, D., Skwarek-Maruszewska, A., Zemanek-Zboch, M. and Laszkiewicz, M.M-B. (2005) 'Beta-actin in human colon adenocarcinoma cell lines with different metastatic potential', Acta Biochim Pol., Vol. 52, No. 2, pp.461-468. (Pubitemid 41133782)
21. Ostlund, G., Lindskog, M. and Sonnhammer, E.L.L. (2010) 'Network-based identification of novel cancer genes', Mol. Cell Proteomics, Vol. 9, No. 4, April, pp.648-655.
22. Popow, A., Nowak, D. and Laszkiewicz, M.M-B. (2006) 'Actin cytoskeleton and betaactin expression in correlation with higher invasiveness of selected hepatoma morris 5123 cells', J. Physiol Pharmacol, Vol. 57, Suppl. 7, November, pp.111-123. (Pubitemid 46548793)
23. Keshava Prasad, T.S., Kandasamy, K. and Pandey, A. (2009) 'Human protein reference database and human proteinpedia as discovery tools for systems biology', Methods Mol. Biol., Vol. 577, pp.67-79.
24. Rosanò, L., Cianfrocca, R., Masi, S., Spinella, F., Di Castro, V., Biroccio, A., Salvati, E., Nicotra, M.R., Natali, P.G. and Bagnato, A. (2009) 'Beta-arrestin links endothelin a receptor to beta-catenin signaling to induce ovarian cancer cell invasion and metastasis', Proc. Natl. Acad. Sci. USA, Vol. 106, No. 8, February, pp.2806-2811. .
25. 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. and Vidal, M. (2005) 'Towards a proteome-scale map of the human protein-protein interaction network', Nature, Vol. 437, No. 7062, October, pp.1173-1178. (Pubitemid 41509356)
26. Ruan, W. and Lai, M. (2007) 'Actin, a reliable marker of internal control?', Clin. Chim. Acta., Vol. 385, Nos. 1-2, October, pp.1-5. (Pubitemid 47374670)
27. Sagynaliev, E., Steinert, R., Nestler, G., Lippert, H., Knoch, M. and Reymond, M-A. (2005) 'Web-based data warehouse on gene expression in human colorectal cancer', Proteomics, Vol. 5, No. 12, August, pp.3066-3078. (Pubitemid 41176473)
28. Schwikowski, B., Uetz, P. and Fields, S. (2000) 'A network of protein-protein interactions in yeast', Nat. Biotechnol., Vol. 18, No. 12, December, pp.1257-1261.
29. Shilov, I.V., Seymour, S.L., Patel, A.A., Loboda, A., Tang, W.H.., Keating, S.P., Hunter, C.L., Nuwaysir, L.M. and Schaeffer, D.A. (2007) 'The paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra', Mol. Cell Proteomics, Vol. 6, No. 9, September, pp.1638-1655. (Pubitemid 47506173)
30. Sonoda, T., Shirabe, K., Takenaka, K., Kanematsu, T., Yasumori, K. and Sugimachi, K. (1989) 'Angiographically undetected small hepatocellular carcinoma: clinicopathological characteristics, follow-up and treatment', Hepatology, Vol. 10, No. 6, December, pp.1003-1007. (Pubitemid 20341091)
31. Stark, C., Breitkreutz, B-J., Reguly, T., Boucher, L., Breitkreutz, A. and Tyers, M. (2006) 'Biogrid: a general repository for interaction datasets', Nucleic Acids Res., Vol. 34, Database issue, January, D535-D539.
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., Toksöz, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H. and Wanker, E.E. (2005) 'A human proteinprotein interaction network: a resource for annotating the proteome', Cell, Vol. 122, No. 6, September, pp.957-968.
33. Tan, H.T., Tan, S., Lin, Q., Lim, T.K., Hew, C.L. and Chung, M.C.M. (2008) 'Quantitative and temporal proteome analysis of butyratetreated colorectal cancer cells', Mol. Cell Proteomics, Vol. 7, No. 6, June, pp.1174-1185. (Pubitemid 351943963)
34. Villanueva, A., Minguez, B., Forner, A., Reig, M. and Llovet, J.M. (2010) 'Hepatocellular carcinoma: novel molecular approaches for diagnosis, prognosis, and therapy', Annu Rev. Med., Vol. 61, pp.317-328.
35. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. and Bork, P. (2002) 'Comparative assessment of large-scale data sets of protein-protein interactions', Nature, Vol. 417, No. 6887, May, pp.399-403. (Pubitemid 34563526)
36. Xenarios, I., Salẃ nski, L., Duan, X.J., Higney, P., Kim, S-M. and Eisenberg, D. (2002) 'Dip, the database of interacting proteins: a research tool for studying cellular networks of protein interactions', Nucleic Acids Res., Vol. 30, No. 1, January, pp.303-305. (Pubitemid 34679570)
37. Zhou, X., Kao, M-C.J. and Wong, W.H. (2002) 'Transitive functional annotation by shortest-path analysis of gene expression data', Proc. Natl. Acad. Sci. USA, Vol. 99, No. 20, October, pp.12783-12788.