Identifying protein interaction subnetworks by a bagging Markov random field-based method

Nucleic Acids Research

Volumn 41, Issue 2, 2013, Pages

  Chen, Li ^a   Xuan, Jianhua ^a,b,c   Riggins, Rebecca B ^a   Wang, Yue ^a   Clarke, Robert ^a  

^a State University   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

^c GEORGETOWN UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN RECEPTOR ALPHA; TAMOXIFEN;

ALGORITHM; ARTICLE; BAGGING MARKOV RANDOM FIELD; BREAST CANCER; CANCER CELL CULTURE; CANCER GROWTH; CONTROLLED STUDY; GENE EXPRESSION; GENE INTERACTION; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SIMULATION; THERAPY RESISTANCE;

ANTINEOPLASTIC AGENTS, HORMONAL; BREAST NEOPLASMS; CELL LINE, TUMOR; DRUG RESISTANCE, NEOPLASM; FEMALE; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; MARKOV CHAINS; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; TAMOXIFEN;

EID: 84875465055     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks951     Document Type: Article

References (48)

1. Hanash, S. (2004) Integrated global profiling of cancer. Nat. Rev. Cancer, 4, 638-644. (Pubitemid 39025058)
2. Richard, O.D., Peter, E.H. and Stork, D.G. (2001) Pattern Classification, 2nd edn. Wiley, New York.
3. Tusher, V.G., Tibshirani, R. and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA, 98, 5116-5121. (Pubitemid 32397092)
4. Kittler, J. (1978) Pattern Recognition and Signal Processing, Chapter Feature Set Search Algorithms. Sijthoff and Noordhoff, Alphen aan den Rijn, Netherlands.
5. Ewens, W.J. and Grant, G.R. (2001) Statistical Methods in Bioinformatics, 1st edn. Springer, New York.
6. Likic, V.A., McConville, M.J., Lithgow, T. and Bacic, A. (2010) Systems biology: the next frontier for bioinformatics. Adv. Bioinformatics, 268925.
7. Chen, L., Xuan, J., Riggins, R.B., Wang, Y., Hoffman, E.P. and Clarke, R. (2010) Multilevel support vector regression analysis to identify condition-specific regulatory networks. Bioinformatics, 26, 1416-1422.
8. Bussemaker, H.J., Li, H. and Siggia, E.D. (2001) Regulatory element detection using correlation with expression. Nat. Genet., 27, 167-171. (Pubitemid 32157443)
9. Bo, T. and Jonassen, I. (2002) New feature subset selection procedures for classification of expression profiles. Genome Biol., 3, RESEARCH0017.
10. Curtis, R.K., Oresic, M. and Vidal-Puig, A. (2005) Pathways to the analysis of microarray data. Trends Biotechnol., 23, 429-435. (Pubitemid 41032923)
11. Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550. (Pubitemid 41528093)
12. Chuang, H.Y., Lee, E., Liu, Y.T., Lee, D. and Ideker, T. (2007) Network-based classification of breast cancer metastasis. Mol. Syst. Biol., 3, 140.
13. Dittrich, M.T., Klau, G.W., Rosenwald, A., Dandekar, T. and Muller, T. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics, 24, i223-i231. (Pubitemid 351911677)
14. Ideker, T., Ozier, O., Schwikowski, B. and Siegel, A.F. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18(Suppl.1), S233-S240. (Pubitemid 41185658)
15. Taylor, I.W., Linding, R., Warde-Farley, D., Liu, Y., Pesquita, C., Faria, D., Bull, S., Pawson, T., Morris, Q. and Wrana, J.L. (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat. Biotechnol., 27, 199-204.
16. Rajagopalan, D. and Agarwal, P. (2005) Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics, 21, 788-793. (Pubitemid 40439415)
17. Clarke, R., Ressom, H.W., Wang, A., Xuan, J., Liu, M.C., Gehan, E.A. and Wang, Y. (2008) The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nat. Rev. Cancer, 8, 37-49.
18. Ein-Dor, L., Zuk, O. and Domany, E. (2006) Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc. Natl Acad. Sci. USA, 103, 5923-5928.
19. Ein-Dor, L., Kela, I., Getz, G., Givol, D. and Domany, E. (2005) Outcome signature genes in breast cancer: is there a unique set? Bioinformatics, 21, 171-178. (Pubitemid 40202018)
20. Wei, Z. and Li, H. (2007) A Markov random field model for network-based analysis of genomic data. Bioinformatics, 23, 1537-1544. (Pubitemid 47244479)
21. Deng, M., Zhang, K., Mehta, S., Chen, T. and Sun, F. (2003) Prediction of protein function using protein-protein interaction data. J. Comput. Biol., 10, 947-960. (Pubitemid 38156407)
22. Breiman, L. (1996) Bagging predictors. Mach. Learn., 24, 123-140. (Pubitemid 126724382)
23. de Matos Simoes, R. and Emmert-Streib, F. (2012) Bagging statistical network inference from large-scale gene expression data. PLoS One, 7, e33624.
24. Hammersley, J. and Clifford, P. (1971) Markov Fields on Finite Graphs and Lattices, Unpublished.
25. Chen, L., Xuan, J., Gu, J., Wang, Y., Zhang, Z., Wang, T.L. and Shih Ie, M. (2012) Integrative network analysis to identify aberrant pathway networks in ovarian cancer. Pac. Symp. Biocomput, 31-42.
26. Li, C. and Li, H. (2008) Network-constrained regularization and variable selection for analysis of genomic data. Bioinformatics, 24, 1175-1182. (Pubitemid 351594167)
27. Kirkpatrick, S., Gelatt, C.D. Jr and Vecchi, M.P. (1983) Optimization by simulated annealing. Science, 220, 671-680.
28. Cerny, V. (1985) Thermodynamical approach to the traveling salesman problem: an efficient simulation algorithm. J. Optim. Theory Appl., 45, 41-51. (Pubitemid 15462741)
29. Efron, B. and Tibshirani, R.J. (1993) An Introduction to the Bootstrap. Chapman and Hall, London.
30. Friedman, N., Linial, M., Nachman, I. and Pe'er, D. (2000) Using Bayesian networks to analyze expression data. J. Comput. Biol., 7, 601-620.
31. Newton, M.A., Kendziorski, C.M., Richmond, C.S., Blattner, F.R. and Tsui, K.W. (2001) On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Comput. Biol., 8, 37-52. (Pubitemid 32679478)
32. van Rijsbergen, C.V. (1979) Information Retrieval, 2nd edn. Butterworth, London.
33. Emmert-Streib, F. and Altay, G. (2010) Local network-based measures to assess the inferability of different regulatory networks. IET Syst. Biol., 4, 277-288.
34. van de Vijver, M.J., He, Y.D., van't Veer, L.J., Dai, H., Hart, A.A., Voskuil, D.W., Schreiber, G.J., Peterse, J.L., Roberts, C., Marton, M.J. et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med., 347, 1999-2009. (Pubitemid 35461656)
35. Wang, Y., Klijn, J.G., Zhang, Y., Sieuwerts, A.M., Look, M.P., Yang, F., Talantov, D., Timmermans, M., Meijer-van Gelder, M.E., Yu, J. et al. (2005) Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet, 365, 671-679. (Pubitemid 40260888)
36. Mishra, G.R., Suresh, M., Kumaran, K., Kannabiran, N., Suresh, S., Bala, P., Shivakumar, K., Anuradha, N., Reddy, R., Raghavan, T.M. et al. (2006) Human protein reference database-2006 update. Nucleic Acids Res., 34, D411-D414.
37. Chen, L., Xuan, J., Riggins, R.B., Clarke, R. and Wang, Y. (2011) Identifying cancer biomarkers by network-constrained support vector machines. BMC Syst. Biol., 5, 161.
38. Gonzalez, L.O., Corte, M.D., Vazquez, J., Junquera, S., Sanchez, R., Alvarez, A.C., Rodriguez, J.C., Lamelas, M.L. and Vizoso, F.J. (2008) Androgen receptor expresion in breast cancer: relationship with clinicopathological characteristics of the tumors, prognosis, and expression of metalloproteases and their inhibitors. BMC Cancer, 8, 149.
39. Rebhan, M., Chalifa-Caspi, V., Prilusky, J. and Lancet, D. (1997) GeneCards: integrating information about genes, proteins and diseases. Trends Genet., 13, 163. (Pubitemid 127739947)
40. Callagy, G.M., Pharoah, P.D., Pinder, S.E., Hsu, F.D., Nielsen, T.O., Ragaz, J., Ellis, I.O., Huntsman, D. and Caldas, C. (2006) Bcl-2 is a prognostic marker in breast cancer independently of the Nottingham Prognostic Index. Clin. Cancer Res., 12, 2468-2475.
41. Loi, S., Haibe-Kains, B., Desmedt, C., Wirapati, P., Lallemand, F., Tutt, A.M., Gillet, C., Ellis, P., Ryder, K., Reid, J.F. et al. (2008) Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics, 9, 239.
42. Symmans, W.F., Hatzis, C., Sotiriou, C., Andre, F., Peintinger, F., Regitnig, P., Daxenbichler, G., Desmedt, C., Domont, J., Marth, C. et al. (2010) Genomic index of sensitivity to endocrine therapy for breast cancer. J. Clin. Oncol., 28, 4111-4119.
43. Affymetrix. (2005) Guide to Probe Logarithmic Intensity Error (PLIER) Estimation, Affymetrix, Santa Clara, CA.
44. Giordano, C., Catalano, S., Panza, S., Vizza, D., Barone, I., Bonofiglio, D., Gelsomino, L., Rizza, P., Fuqua, S.A. and Ando, S. (2011) Farnesoid X receptor inhibits tamoxifen-resistant MCF-7 breast cancer cell growth through downregulation of HER2 expression. Oncogene, 30, 4129-4140.
45. Kurokawa, H., Lenferink, A.E., Simpson, J.F., Pisacane, P.I., Sliwkowski, M.X., Forbes, J.T. and Arteaga, C.L. (2000) Inhibition of HER2/neu (erbB-2) and mitogen-activated protein kinases enhances tamoxifen action against HER2-overexpressing, tamoxifen-resistant breast cancer cells. Cancer Res., 60, 5887-5894.
46. Creighton, C.J., Cordero, K.E., Larios, J.M., Miller, R.S., Johnson, M.D., Chinnaiyan, A.M., Lippman, M.E. and Rae, J.M. (2006) Genes regulated by estrogen in breast tumor cells in vitro are similarly regulated in vivo in tumor xenografts and human breast tumors. Genome Biol., 7, R28.
47. Aguilar, H., Sole, X., Bonifaci, N., Serra-Musach, J., Islam, A., Lopez-Bigas, N., Mendez-Pertuz, M., Beijersbergen, R.L., Lazaro, C., Urruticoechea, A. et al. (2010) Biological reprogramming in acquired resistance to endocrine therapy of breast cancer. Oncogene, 29, 6071-6083.
48. Barrios, C., Forbes, J.F., Jonat, W., Conte, P., Gradishar, W., Buzdar, A., Gelmon, K., Gnant, M., Bonneterre, J., Toi, M. et al. (2012) The sequential use of endocrine treatment for advanced breast cancer: where are we? Ann. Oncol., 23, 1378-1386.