Coregulation of transcription factors and microRNAs in human transcriptional regulatory network

BMC Bioinformatics

Research

Chiou-Shann Fuh¹  Hsueh-Fen Juan²  Shui-Tein Chen³  Hsuan-Cheng Huang⁴  Cho-Yi Chen⁵ 

[1] Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan;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;Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan;Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan;Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan;Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan;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;

关键词: Functional Enrichment;    Network Motif;    Edge Type;    Specific Biological Process;    Shared Target;   

DOI  :  10.1186/1471-2105-12-S1-S41

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (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.MethodsWe 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.ResultsWe 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.ConclusionOur 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.

【 授权许可】

Unknown   
© Chen et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.