Open Access Highly Accessed Research article

Regulatory coordination of clustered microRNAs based on microRNA-transcription factor regulatory network

Jin Wang1, Martin Haubrock2, Kun-Ming Cao1, Xu Hua1, Chen-Yu Zhang1*, Edgar Wingender2* and Jie Li1*

Author Affiliations

1 The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology

2 Department of Bioinformatics, Medical School, Georg August University of Göttingen, Goldschmidtstrasse 1, D-37077 Göttingen, Germany

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BMC Systems Biology 2011, 5:199  doi:10.1186/1752-0509-5-199

Published: 16 December 2011

Additional files

Additional file 1:

miRNA clusters. All of the 66 miRNA clusters are listed associating with their types, i.e. homo-cluster or hetro-cluster.

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Additional file 2:

Distribution of target overlaps for homologous miRNAs. The black is for the homologous miRNAs in homo-clusters, and the red for all the homologous miRNAs.

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Additional file 3:

Examples of 3-steps coordinated regulation of hetero-clustered miRNAs. Six examples embedding the cross-regulation between intermediate regulators are illustrated.

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Additional file 4:

MiRNA clusters composed of intronic/extronic miRNAs. The information about miRNA types and host genes of intronic/extronic clustered miRNAs is derived from miRBase 13.0.

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Additional file 5:

Direct regulatory coordination for two types of intergenic miRNA clusters. Target overlap (TO) distribution describing the direct regulatory coordination. a) for our intergenic miRNA clusters; b) for 4 kbp-constraint intergenic miRNA clusters. The black, red and blue plots are respectively for the homo-clustered, hetero-clustered and randomized miRNA pairs (i.e. the miRNA pairs randomly selected from different intergenic miRNA clusters) that are located in intergenic miRNA clusters. The TO distributions show a similar behavior in figure a) and b), suggesting that the definition of the intergenic miRNA clusters has no impact on the property of the direct regulatory coordination.

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Additional file 6:

Indirect regulatory coordination for two types of intergenic miRNA clusters. TO distribution describing the indirect regulatory coordination. a) for our intergenic miRNA clusters; b) for 4 kbp-constraint intergenic miRNA clusters. The black, red and blue plots are respectively for the homo-clustered, hetero-clustered and randomized miRNA pairs that are located in intergenic miRNA clusters. The TO distributions show a similar behavior in figure a) and b), suggesting that the definition of the intergenic miRNA clusters has no impact on the property of the indirect regulatory coordination.

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Additional file 7:

Regulatory network. The whole regulatory network is provided in SIF format.

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Additional file 8:

Enriched functions of targets of homo-clustered miRNAs. Detailed information about the enriched functions of the targets of homo-clustered miRNAs is given.

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Additional file 9:

Enriched functions of targets of hetero-clustered miRNAs. Detailed information about the enriched functions of the targets of hetero-clustered miRNAs is given.

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