Construction and investigation of breast-cancerspecific ceRNA network based on the mRNA and miRNA expression data

IET Systems Biology

Volumn 8, Issue 3, 2014, Pages 96-103

  Zhou, Xionghui ^a   Liu, Juan ^a   Wang, Wei ^a  

^a WUHAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION (OF INFORMATION); DISEASES; GENES;

BIOLOGICAL FUNCTIONS; BIOLOGICAL MECHANISMS; DENSE CLUSTERS; DISTANT METASTASIS; MESSENGER RNA; MIRNA EXPRESSIONS; MRNA EXPRESSION; NETWORK-BASED;

RNA;

MESSENGER RNA; MICRORNA;

ALGORITHM; ARTICLE; BIOLOGY; BREAST TUMOR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; HUMAN; HUMAN GENOME; METABOLISM; METASTASIS; METHODOLOGY;

ALGORITHMS; BREAST NEOPLASMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GENOME, HUMAN; HUMANS; MICRORNAS; NEOPLASM METASTASIS; RNA, MESSENGER;

EID: 84906931020     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2013.0025     Document Type: Article

References (41)

1. Baek, D., Villen, J., Shin, C., Camargo, F.D., Gygi, S.P., Bartel, D.P.:'The impact of microRNAs on protein output', Nature, 2008, 455, pp. 64-71
2. Chen, C.Z., Li, L., Lodish, H.F., Bartel, D.P.:'MicroRNAs modulate hematopoietic lineage differentiation', Science, 2004, 303, pp. 83-86
3. Schmittgen, T.D.:'Regulation of microRNA processing in development, differentiation and cancer', J. Cell. Mol. Med., 2008, 12, pp. 1811-1819
4. Salmena, L., Poliseno, L., Tay, Y., Kats, L., Pandolfi, P.P.:'A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?', Cell, 2011, 146, pp. 353-358
5. Ala, U., Karreth, F.A., Bosia, C., et al.:'Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments', Proc. Natl. Acad. Sci. USA, 2013, 110, pp. 7154-7159
6. Tay, Y., Kats, L., Salmena, L., et al.:'Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs', Cell, 2011, 147, pp. 344-357
7. Liu, K., Yan, Z., Li, Y., Sun, Z.:'Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis', Bioinformatics, 2013, 29, pp. 2221-2222
8. Muniategui, A., Pey, J., Planes, F.J., Rubio, A.:'Joint analysis of miRNA and mRNA expression data', Brief. Bioinf., 2013, 14, pp. 263-278
9. Clarke, C., Henry, M., Doolan, P., et al.:'Integrated miRNA, mRNA and protein expression analysis reveals the role of post-transcriptional regulation in controlling CHO cell growth rate', BMC Genomics, 2012, 13, p. 656
10. Stuart, J.M., Segal, E., Koller, D., Kim, S.K.:'A gene-coexpression network for global discovery of conserved genetic modules', Science, 2003, 302, pp. 249-255
11. Wang, Y.X., Klijn, J.G.M., Zhang, Y., et al.:'Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer', Lancet, 2005, 365, pp. 671-679
12. van de Vijver, M.J., He, Y.D., van't Veer, L.J., et al.:'A gene-expression signature as a predictor of survival in breast cancer', N. Engl. J. Med., 2002, 347, pp. 1999-2009
13. Miller, L.D., Smeds, J., George, J., et al.:'An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival', Proc. Natl. Acad. Sci. USA, 2005, 102, pp. 13550-13555
14. Chuang, H.Y., Lee, E., Liu, Y.T., Lee, D., Ideker, T.:'Network-based classification of breast cancer metastasis', Mol. Syst. Biol., 2007, 3, p. 140
15. Venet, D., Dumont, J.E., Detours, V.:'Most random gene expression signatures are significantly associated with breast cancer outcome', PLoS Comput. Biol., 2011, 7, p. e1002240
16. Enerly, E., Steinfeld, I., Kleivi, K., et al.:'miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors', PLoS One, 2011, 6, p. e16915
17. Pawitan, Y., Bjohle, J., Amler, L., et al.:'Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts', Breast Cancer Res., 2005, 7, pp. R953-R964
18. Ivshina, A.V., George, J., Senko, O., et al.:'Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer', Cancer Res., 2006, 66, pp. 10292-10301
19. Desmedt, C., Piette, F., Loi, S., et al.:'Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series', Clin. Cancer Res., 2007, 13, pp. 3207-3214
20. Garcia, D.M., Baek, D., Shin, C., Bell, G.W., Grimson, A., Bartel, D.P.:'Weak seed-pairing stability and high target-site abundance decrease the proficiency of Lsy-6 and other microRNAs', Nat. Struct. Mol. Biol., 2011, 18, pp. 1139-1146
21. Betel, D., Koppal, A., Agius, P., Sander, C., Leslie, C.:'Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites', Genome Biol., 2010, 11, p. R90
22. Assenov, Y., Ramirez, F., Schelhorn, S.E., Lengauer, T., Albrecht, M.:'Computing topological parameters of biological networks', Bioinformatics, 2008, 24, pp. 282-284
23. Bader, G.D., Hogue, C.W.:'An automated method for finding molecular complexes in large protein interaction networks', BMC Bioinf., 2003, 4, p. 2
24. Hase, T., Tanaka, H., Suzuki, Y., Nakagawa, S., Kitano, H.:'Structure of protein interaction networks and their implications on drug design', PLoS Comput. Biol., 2009, 5, p. e1000550
25. Giaever, G., Chu, A.M., Ni, L., et al.:'Functional profiling of the Saccharomyces cerevisiae genome', Nature, 2002, 418, pp. 387-391
26. Song, J.M., Singh, M.:'From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization', PLoS Comput. Biol., 2013, 9, p. e1002910
27. Hahn, M.W., Kern, A.D.:'Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks', Mol. Biol. Evol., 2005, 22, pp. 803-806
28. Huang, D.W., Sherman, B.T., Lempicki, R.A.:'Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources', Nat. Protocols, 2009, 4, pp. 44-57
29. Sotiriou, C., Wirapati, P., Loi, S., et al.:'Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis', J. Natl. Cancer Inst., 2006, 98, pp. 262-272
30. Cardillo, G.:'LogRank: Comparing survival curves of two groups using the log rank test', 2008
31. Jain, R.K.:'Normalization of tumor vasculature: an emerging concept in antiangiogenic therapy', Science, 2005, 307, pp. 58-62
32. Hlavaty, J., Petznek, H., Holzmuller, H., et al.:'Evaluation of a gene-directed enzyme-product therapy (GDEPT) in human pancreatic tumor cells and their use as in vivo models for pancreatic cancer', PLoS One, 2012, 7, p. e40611
33. Dachs, G.U., Tupper, J., Tozer, G.M.:'From bench to bedside for gene-directed enzyme prodrug therapy of cancer', Anti-Cancer Drugs, 2005, 16, pp. 349-359
34. Ward, P.S., Thompson, C.B.:'Metabolic reprogramming: a cancer hallmark even Warburg did not anticipate', Cancer Cell, 2012, 21, pp. 297-308
35. Preston-Martin, S., Pike, M.C., Ross, R.K., Jones, P.A., Henderson, B. E.:'Increased cell division as a cause of human cancer', Cancer Research, 1990, 50, pp. 7415-7421
36. Bos, P.D., Zhang, X.H.F., Nadal, C., et al.:'Genes that mediate breast cancer metastasis to the brain', Nature, 2009, 459, pp. 1005-1009
37. Saharinen, P., Tammela, T., Karkkainen, M.J., Alitalo, K.:'Lymphatic vasculature: development, molecular regulation and role in tumor metastasis and inflammation', Trends Immunol., 2004, 25, pp. 387-395
38. Baluk, P., Hashizume, H., McDonald, D.M.:'Cellular abnormalities of blood vessels as targets in cancer', Curr. Opin. Genet. Dev., 2005, 15, pp. 102-111
39. Parri, M., Chiarugi, P.:'Rac and Rho GTPases in cancer cell motility control', Cell Commun. Signal., 2010, 8, p. 23
40. Peng, K., Xu, W., Zheng, J., et al.:'The disease and gene annotations (DGA): an annotation resource for human disease', Nucl. Acids Res., 2013, 41, pp. D553-60
41. Storey, J.D.: 'A direct approach to false discovery rates', J. R. Stat. Soc. Ser. B-Stat. Methodol., 2002, 64, pp. 479-498