ArticleBMC genomics2013
Understanding cooperativity of microRNAs via microRNA association networks.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- SiCmiR Atlas: Single-Cell miRNA Landscape Reveals Hub-miRNA and Network Signatures in Human Cancers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Conjunctival MicroRNA Expression Signature in Primary Sjögren's Syndrome Dry Eye: A NanoString-Based Bioinformatic Analysis.Investigative ophthalmology & visual science · 2025Article
- Influenza a virus regulates interferon signaling and its associated genes; MxA and STAT3 by cellular miR-141 to ensure viral replication.Virology journal · 2023Article
- Review
- Non-coding RNA in rhabdomyosarcoma progression and metastasis.Frontiers in oncology · 2022Review
- circ_SEPT9, a newly identified circular RNA, promotes oral squamous cell carcinoma progression through miR-1225/PKN2 axis.Journal of cellular and molecular medicine · 2020Article
- Biomarkers in traumatic brain injury: new concepts.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2020Review
- MiRNA Regulatory Functions in Photoreceptors.Frontiers in cell and developmental biology · 2020Review
- MicroRNA-Based Combinatorial Cancer Therapy: Effects of MicroRNAs on the Efficacy of Anti-Cancer Therapies.Cells · 2019Review
- Integrated Analysis of microRNA and mRNA Expression Profiles: An Attempt to Disentangle the Complex Interaction Network in Attention Deficit Hyperactivity Disorder.Brain sciences · 2019Article
- Genomic non-redundancy of the mir-183/96/182 cluster and its requirement for hair cell maintenance.Scientific reports · 2019Article
- Investigating the Role of MicroRNA and Transcription Factor Co-regulatory Networks in Multiple Sclerosis Pathogenesis.International journal of molecular sciences · 2018Article
- Interferon down-regulation of miR-1225-3p as an antiviral mechanism through modulating Grb2-associated binding protein 3 expression.The Journal of biological chemistry · 2018Article
- Role of MicroRNAs in Obesity-Induced Metabolic Disorder and Immune Response.Journal of immunology research · 2018Review
- Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach.Scientific reports · 2017Article
- Co-Expression Network and Pathway Analyses Reveal Important Modules of miRNAs Regulating Milk Yield and Component Traits.International journal of molecular sciences · 2017Article
- miR-144 attenuates the host response to influenza virus by targeting the TRAF6-IRF7 signaling axis.PLoS pathogens · 2017Article
- Article
- MicroRNAs as regulatory elements in immune system logic.Nature reviews. Immunology · 2016Review
- Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroRNAs (miRNAs) are key components in post-transcriptional gene regulation in multicellular organisms. As they control cooperatively a large number of their target genes, they affect the complexity of gene regulation. One of the challenges to understand miRNA-mediated regulation is to identify co-regulating miRNAs that simultaneously regulate their target genes in a network perspective.
resultsWe created miRNA association network by using miRNAs sharing target genes based on sequence complementarity and co-expression patterns of miRNA-target pairs. The degree of association between miRNAs can be assessed by the level of concordance between targets of miRNAs. Cooperatively regulating miRNAs have been identified by network topology-based approach. Cooperativity of miRNAs is evaluated by their shared transcription factors and functional coherence of target genes. Pathway enrichment analysis of target genes in the cooperatively regulating miRNAs revealed the mutually exclusive functional landscape of miRNA cooperativity. In addition, we found that one miRNA in the miRNA association network could be involved in many cooperatively regulating miRNAs in a condition-specific and combinatorial manner. Sequence and structural similarity analysis within miRNA association network showed that pre-miRNA secondary structure may be involved in the expression of mature miRNA's function.
conclusionsOn the system level, we identified cooperatively regulating miRNAs in the miRNA association network. We showed that the secondary structures of pre-miRNAs in cooperatively regulating miRNAs are highly similar. This study demonstrates the potential importance of the secondary structures of pre-miRNAs in both cooperativity and specificity of target genes.
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