ArticleBMC systems biology2009
Clustered microRNAs' coordination in regulating protein-protein interaction network.
Article in BMC systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Advancing Ischemic Stroke Prognosis: Key Role of MiR-155 Non-Coding RNA.International journal of molecular sciences · 2025Review
- Modeling ncRNA Synergistic Regulation in Cancer.Methods in molecular biology (Clifton, N.J.) · 2025Review
- The Clinical Significance of MicroRNAs in Colorectal Cancer Signaling Pathways: A Review.Global medical genetics · 2023Review
- Characterization of microRNAs in the cyst nematodeRNA biology · 2023Article
- Tumor elimination by clustered microRNAs miR-306 and miR-79 via noncanonical activation of JNK signaling.eLife · 2022Article
- Diagnostic and Prognostic Potential of MiR-379/656 MicroRNA Cluster in Molecular Subtypes of Breast Cancer.Journal of clinical medicine · 2021Article
- Loss of miR-183/96 Alters Synaptic Strength via Presynaptic and Postsynaptic Mechanisms at a Central Synapse.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2021Article
- Review
- Global analysis of SBP gene family in Brachypodium distachyon reveals its association with spike development.Scientific reports · 2020Article
- Article
- Identifying miRNA synergism using multiple-intervention causal inference.BMC bioinformatics · 2019Article
- Conservation and novelty in the microRNA genomic landscape of hyperdiverse cichlid fishes.Scientific reports · 2019Article
- Comprehensive Investigation of miRNome Identifies Novel Candidate miRNA-mRNA Interactions Implicated in T-Cell Acute Lymphoblastic Leukemia.Neoplasia (New York, N.Y.) · 2019Article
- In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.Scientific reports · 2018Article
- Integrative analysis of dysregulated microRNAs and mRNAs in multiple recurrent synchronized renal tumors from patients with von Hippel-Lindau disease.International journal of oncology · 2018Article
- MicroRNA-23a/27a/24-2 cluster promotes gastric cancer cell proliferation synergistically.Oncology letters · 2018Article
- ceRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins.Scientific reports · 2017Article
- SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data.International journal of molecular sciences · 2017Article
- A network-biology perspective of microRNA function and dysfunction in cancer.Nature reviews. Genetics · 2016Review
- microRNAs in the Same Clusters Evolve to Coordinately Regulate Functionally Related Genes.Molecular biology and evolution · 2016Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroRNAs (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.
resultsIntegrating 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.
conclusionIn summary, this work supports the hypothesis of intra-cluster coordination and investigates the extent of this coordination.
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