Combining Gene Expression and Interactions Data with miRNA Family Information for Identifying miRNA-mRNA Regulatory Modules
It is well known that microRNAs (miRNAs) play pivotal roles in gene expression, transcriptional regulation and other important biological processes. An impressive body of literature indicates that miRNAs and mRNAs work cooperatively to form an important part of gene regulatory modules which are extensively involved in cancer. However, with the accumulation of available data, it is a great challenge to identify cancer-related miRNA regulatory modules and uncover their precise regulatory mechanism. This paper proposed a novel computational framework by combining gene expression and interaction data with miRNA family information to identify miRNA-mRNA regulatory modules (GIFMRM), which was evaluated on three heterogeneous datasets. Literature survey, biological significance and functional enrichment analysis were used to validate the obtained results. The analysis results show that the modules identified are highly correlated with the biological conditions in their respective datasets, and they enrich in GO biological processes and KEGG pathways.
KeywordsmiRNA-mRNA regulation modules Gene expression miRNA family
This work was supported by the grants of the National Science Foundation of China (Grant Nos. 61472467, 61672011, and 61471169) and the Collaboration and Innovation Center for Digital Chinese Medicine of 2011 Project of Colleges and Universities in Hunan Province.
- 8.Yoon, S.R., De Micheli, G.: Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics 21(2), 93–100 (2005)Google Scholar
- 15.Borgatti, S.P.: How to explain hierarchical clustering (1994)Google Scholar
- 16.Sokal, R.R.: A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull. 28, 1409–1438 (1958)Google Scholar
- 18.Vetter, G., Saumet, A., Moes, M., Vallar, L., Béchec, A.L., Laurini, C., Sabbah, M., Arar, K., Theillet, C., Lecellier, C.H.: miR-661 expression in SNAI1-induced epithelial to mesenchymal transition contributes to breast cancer cell invasion by targeting nectin-1 and stard10 messengers. Oncogene 29(31), 4436 (2010)CrossRefGoogle Scholar
- 21.Zhang, Q.: Role of Jak/Stat pathway in the pathogenesis of breast cancer (2010)Google Scholar
- 23.Lee, C., Fan, S., Sit, W., Jor, I.W., Wong, L.L., Man, K., Tan-Un, K., Wan, J.M.: Olive oil enriched diet suppresses hepatocellular carcinoma (Hcc) tumor growth via focal adhesion pathway. Cancer Res. 67(9 Supplement), LB-60 (2007)Google Scholar