This article is part of the supplement: Selected articles from the Ninth Asia Pacific Bioinformatics Conference (APBC 2011)
Research
Coregulation of transcription factors and microRNAs in human transcriptional regulatory network
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* Corresponding authors: Hsueh-Fen Juan yukijuan@ntu.edu.tw - Hsuan-Cheng Huang hsuancheng@ym.edu.tw
1 Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
2 Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
3 Genome and Systems Biology Degree Program, Department of Life Science, Institute of Molecular and Cellular Biology, Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
4 Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
BMC Bioinformatics 2011, 12(Suppl 1):S41 doi:10.1186/1471-2105-12-S1-S41
Published: 15 February 2011Abstract
Background
MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression at the post-transcriptional level. Recent studies have suggested that miRNAs and transcription factors are primary metazoan gene regulators; however, the crosstalk between them still remains unclear.
Methods
We proposed a novel model utilizing functional annotation information to identify significant coregulation between transcriptional and post-transcriptional layers. Based on this model, function-enriched coregulation relationships were discovered and combined into different kinds of functional coregulation networks.
Results
We found that miRNAs may engage in a wider diversity of biological processes by coordinating with transcription factors, and this kind of cross-layer coregulation may have higher specificity than intra-layer coregulation. In addition, the coregulation networks reveal several types of network motifs, including feed-forward loops and massive upstream crosstalk. Finally, the expression patterns of these coregulation pairs in normal and tumour tissues were analyzed. Different coregulation types show unique expression correlation trends. More importantly, the disruption of coregulation may be associated with cancers.
Conclusion
Our findings elucidate the combinatorial and cooperative properties of transcription factors and miRNAs regulation, and we proposes that the coordinated regulation may play an important role in many biological processes.