Inferring condition-specific miRNA-Gene modules from miRNA and mRNA profiling data

Jianghui Xiong, Chen Wang, Bai Zhang, Yue Wang, Eric P. Hoffman, Robert Clarke, Jianhua Xuan

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Recently, a class of small RNA molecules, microRNAs or miRNAs, has attracted interest from researchers for their unique role in post-transcriptional regulation. Due to their distinct cell-type/tissue-specific expression patterns, it is of high importance to identify condition-specific miRNA-gene modules for a complete depiction of gene regulatory networks. In this paper, we propose a novel method to integrate miRNA and mRNA data to identify condition-specific miRNA-gene modules. Specifically, a Consistency-based Masking Nonnegative Matrix Factorization (CMNMF) method is developed to incorporate existing biological constraints (like the repression of miRNAs on potential target genes) with simultaneous miRNA and mRNA profiling data for an improved performance in module identification. The experimental results on simulation data show that the condition-specific modeling framework improves the performance in predicting miRNA-gene relationships. More importantly, application of CMNMF to human colon cancer data revealed a biologically significant miRNA-gene module, which contains four up-regulated miRNAs (miR-182, miR-183, miR-221 and miR-222) and six down-regulated target genes annotated as cytotoxity mediated by nature killer cells. The proposed method can also be applied to various biological conditions, even with limited number of samples, to elucidate miRNA-involved gene networks.

Original languageEnglish (US)
Title of host publicationInternational Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2008, BCBGC 2008
Pages49-55
Number of pages7
StatePublished - Dec 1 2008
Event2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, BCBGC 2008 - Orlando, FL, United States
Duration: Jul 7 2008Jul 10 2008

Publication series

NameInternational Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2008, BCBGC 2008

Other

Other2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, BCBGC 2008
CountryUnited States
CityOrlando, FL
Period7/7/087/10/08

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ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Xiong, J., Wang, C., Zhang, B., Wang, Y., Hoffman, E. P., Clarke, R., & Xuan, J. (2008). Inferring condition-specific miRNA-Gene modules from miRNA and mRNA profiling data. In International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2008, BCBGC 2008 (pp. 49-55). (International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2008, BCBGC 2008).