Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation

Bioinformatics

Volumn 26, Issue 24, 2010, Pages 3105-3111

  Liu, Bing ^a,b   Liu, Lin ^a   Tsykin, Anna ^b,c   Goodall, Gregory J ^b,c   Green, Jeffrey E ^d   Zhu, Min ^d   Kim, Chang Hee ^e   Li, Jiuyong ^a  

^a UNIVERSITY OF SOUTH AUSTRALIA   (Australia)

^b INSTITUTE OF MEDICAL AND VETERINARY SCIENCE   (Australia)

^c UNIVERSITY OF ADELAIDE   (Australia)

^d NATIONAL CANCER INSTITUTE   (United States)

^e NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

ANIMAL; ARTICLE; EXPERIMENTAL NEOPLASM; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM; MOUSE; STATISTICAL MODEL;

ANIMALS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; MAMMARY NEOPLASMS, EXPERIMENTAL; MICE; MICRORNAS; MODELS, STATISTICAL; RNA, MESSENGER;

EID: 79951751828     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq576     Document Type: Article

References (36)

1. Adelaide, J. et al. (2007) Integrated profiling of basal and luminal breast cancers. Cancer Res., 67, 11565-11575.
2. Akao, Y. et al. (2007) MicroRNA-143 and -145 in colon cancer. DNA Cell Biol., 26, 311-320.
3. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
4. Bentwich, I. et al. (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet., 37, 766-770.
5. Bergamaschi, A. et al. (2006) Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes, Chromosomes and Cancer, 45, 1033-1040.
6. Blei, D.M. and Jordan, M.I. (2003) Modeling annotated data. In SIGIR '03: Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval, ACM, New York, NY, USA, pp. 127-134.
7. Blenkiron, C. et al. (2007) MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol., 8, R214.
8. Bonnet, E. et al. (2010) Module network inference from a cancer gene expression dataset identifies microRNA regulated modules. PLoS ONE, 5, e10162.
9. Chin, K. et al. (2006) Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell, 10, 529-541.
10. Croce, C.M. (2009) Causes and consequences of microRNA dysregulation in cancer. Nat. Rev. Genet., 10, 704-714.
11. Desai, K.V. et al. (2002) Initiating oncogenic event determines gene-expression patterns of human breast cancer models. Proc. Natl Acad. Sci. USA, 99, 6967-6972.
12. Du, T. and Zamore, P.D. (2007) Beginning to understand microRNA function. Cell Res, 17, 661-663.
13. Griffiths-Jones, S. et al. (2008) mirbase: tools for microRNA genomics. Nucleic Acids Res., 36 (Suppl. 1), D154-158.
14. Hatzigeorgiou, A.G. (2007) Same computational analysis, different miRNA target predictions. Nature Methods, 4, 191.
15. He, L. and Hannon, G.J. (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet., 5, 522-531.
16. Herschkowitz, J. et al. (2007) Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol., 8, R76.
17. Huang, J.C. et al. (2007) Using expression profiling data to identify human microRNA targets. Nat. Methods, 4, 1045-1049.
18. Iorio, M.V. et al. (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res., 65, 7065-7070.
19. Joung, J.-G. and Fei, Z. (2009) Identification of microRNA regulatory modules in arabidopsis via a probabilistic graphical model. Bioinformatics, 25, 387-393.
20. Joung, J.-G. et al. (2007) Discovery of microRNA-mRNAmodules via population-based probabilistic learning. Bioinformatics, 23, 1141-1147.
21. Krek, A. et al. (2005) Combinatorial microRNA target predictions. Nat. Genet., 37, 495-500.
22. Lewis, B.P. et al. (2003) Prediction of mammalian microRNA targets. Cell, 115, 787-798.
23. Lewis, B.P. et al. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
24. Liu, J.S. (1994) The collapsed gibbs sampler in bayesian computations with applications to a gene regulation problem. J. Am. Stat. Assoc., 89, 930-958.
25. Liu, B. et al. (2009a) Discovery of functional miRNA-mRNA regulatory modules with computational methods. J. Biomed. Infor., 42, 685-691.
26. Liu, B. et al. (2009b). Exploring complex miRNA-mRNA interactions with bayesian networks by splitting-averaging strategy. BMC Bioinformatics, 10, 408.
27. Neve, R.M. et al. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell, 10, 515-527.
28. Peng, X. et al. (2009) Computational identification of hepatitis c virus associated microRNA-mRNA regulatory modules in human livers. BMC Genomics, 10, 373.
29. Porkka, K.P. et al. (2007) MicroRNA expression profiling in prostate cancer. Cancer Res., 67, 6130-6135.
30. Steyvers, M. et al. (2004) Probabilistic author-topic models for information discovery. In KDD '04: Proceedings of the tenth ACM SIGKDD international conference on Knowledge discovery and data mining, ACM, New York, NY, USA, pp. 306-315.
31. Tran, D. et al. (2008) Finding microRNA regulatory modules in human genome using rule induction. BMC Bioinformatics, 9 (Suppl. 12), S5.
32. Yanaihara, N. (2006) Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell, 9, 189-198.
33. Yang, H. et al. (2008) MicroRNA expression profiling in human ovarian cancer: miR- 214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer Res., 68, 425-433.
34. Yoon, S. and De Micheli, G. (2005) Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics, 21 (suppl. 2), ii93-ii100.
35. Zhao, Y. and Srivastava, D. (2007) Adevelopmental view of microRNAfunction. Trends Biochem. Sci., 32, 189-197.
36. Zhu, M. et al. (2010) Comprehensive genomic profiling identifies miRNA signatures associated with mouse mammary tumor subtypes. In preparation.