Clustered microRNAs' coordination in regulating protein-protein interaction network Export

@article{citeulike:5011693, abstract = {BACKGROUND:MicroRNAs (miRNAs), a growing class of small RNAs with crucial regulatory roles at the post-transcriptional level, are usually found to be clustered on chromosomes. However, with the exception of a few individual cases, so far little is known about the functional consequence of this conserved clustering of miRNA loci. In animal genomes such clusters often contain non-homologous miRNA genes. One hypothesis to explain this heterogeneity suggests that clustered miRNAs are functionally related by virtue of co-targeting downstream pathways.RESULTS:Integrating of miRNA cluster information with protein protein interaction (PPI) network data, our research supports the hypothesis of the functional coordination of clustered miRNAs and links it to the topological features of miRNAs' targets in PPI network. Specifically, our results demonstrate that clustered miRNAs jointly regulate proteins in close proximity of the PPI network. The possibility that two proteins yield to this coordinated regulation is negatively correlated with their distance in PPI network. Guided by the knowledge of this preference, we found several network communities enriched with target genes of miRNA clusters. In addition, our results demonstrate that the variance of this propensity can also partly be explained by protein's connectivity and miRNA's conservation.CONCLUSIONS:In summary, this work supports the hypothesis of intra-cluster coordination and investigates the extent of this coordination.}, author = {Yuan, Xiongying and Liu, Changning and Yang, Pengcheng and He, Shunmin and Liao, Qi and Kang, Shuli and Zhao, Yi}, citeulike-article-id = {5011693}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1752-0509-3-65}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19558649}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19558649}, day = {26}, doi = {10.1186/1752-0509-3-65}, issn = {1752-0509}, journal = {BMC Systems Biology}, keywords = {cluster, interaction, microrna, network, protein, regulation}, month = {June}, number = {1}, pages = {65+}, posted-at = {2009-06-29 12:44:13}, priority = {2}, title = {Clustered microRNAs' coordination in regulating protein-protein interaction network}, url = {http://dx.doi.org/10.1186/1752-0509-3-65}, volume = {3}, year = {2009} }

TY - JOUR ID - citeulike:5011693 L3 - citeulike-article-id:5011693 N2 - BACKGROUND:MicroRNAs (miRNAs), a growing class of small RNAs with crucial regulatory roles at the post-transcriptional level, are usually found to be clustered on chromosomes. However, with the exception of a few individual cases, so far little is known about the functional consequence of this conserved clustering of miRNA loci. In animal genomes such clusters often contain non-homologous miRNA genes. One hypothesis to explain this heterogeneity suggests that clustered miRNAs are functionally related by virtue of co-targeting downstream pathways.RESULTS:Integrating of miRNA cluster information with protein protein interaction (PPI) network data, our research supports the hypothesis of the functional coordination of clustered miRNAs and links it to the topological features of miRNAs' targets in PPI network. Specifically, our results demonstrate that clustered miRNAs jointly regulate proteins in close proximity of the PPI network. The possibility that two proteins yield to this coordinated regulation is negatively correlated with their distance in PPI network. Guided by the knowledge of this preference, we found several network communities enriched with target genes of miRNA clusters. In addition, our results demonstrate that the variance of this propensity can also partly be explained by protein's connectivity and miRNA's conservation.CONCLUSIONS:In summary, this work supports the hypothesis of intra-cluster coordination and investigates the extent of this coordination. IS - 1 JF - BMC Systems Biology SN - 1752-0509 TI - Clustered microRNAs' coordination in regulating protein-protein interaction network VL - 3 SP - 65 KW - cluster KW - interaction KW - microrna KW - network KW - protein KW - regulation AU - Yuan, Xiongying AU - Liu, Changning AU - Yang, Pengcheng AU - He, Shunmin AU - Liao, Qi AU - Kang, Shuli AU - Zhao, Yi PY - 2009/06/26/ UR - http://dx.doi.org/10.1186/1752-0509-3-65 ER -