ArticleNucleic acids research2012
Context-specific microRNA analysis: identification of functional microRNAs and their mRNA targets.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
- An efficient framework to decipher microRNA regulatory programs applied to T cells.Genes and immunity · 2025Article
- Protocols for Extraction of miRNA from Extracellular Vesicles of Lyophilized Human Saliva Samples.International journal of molecular sciences · 2025Article
- Review
- Aberrant transcriptional and post-transcriptional regulation of SPAG5, a YAP-TAZ-TEAD downstream effector, fuels breast cancer cell proliferation.Cell death and differentiation · 2021Article
- Integrative approaches for analysis of mRNA and microRNA high-throughput data.Computational and structural biotechnology journal · 2021Review
- Elucidation of molecular links between obesity and cancer through microRNA regulation.BMC medical genomics · 2020Article
- A Traditional Korean Diet Alters the Expression of Circulating MicroRNAs Linked to Diabetes Mellitus in a Pilot Trial.Nutrients · 2020Article
- Article
- Integrated Analysis of microRNA and mRNA Expression Profiles: An Attempt to Disentangle the Complex Interaction Network in Attention Deficit Hyperactivity Disorder.Brain sciences · 2019Article
- miR-671-5p inhibits gastric cancer cell proliferation and promotes cell apoptosis by targeting URGCP.Experimental and therapeutic medicine · 2018Article
- Investigating the Role of MicroRNA and Transcription Factor Co-regulatory Networks in Multiple Sclerosis Pathogenesis.International journal of molecular sciences · 2018Article
- Article
- Improving microRNA target prediction with gene expression profiles.BMC genomics · 2016Article
- Polysome shift assay for direct measurement of miRNA inhibition by anti-miRNA drugs.Nucleic acids research · 2016Article
- MicroRNAs in the axon locally mediate the effects of chondroitin sulfate proteoglycans and cGMP on axonal growth.Developmental neurobiology · 2015Article
- The mRNA related ceRNA-ceRNA landscape and significance across 20 major cancer types.Nucleic acids research · 2015Article
- Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential.BMC systems biology · 2015Review
- MicroRNA regulons in tumor microenvironment.Oncogene · 2015Review
- MiR-137 inhibits proliferation and angiogenesis of human glioblastoma cells by targeting EZH2.Journal of neuro-oncology · 2015Article
- miR-186 and 326 predict the prognosis of pancreatic ductal adenocarcinoma and affect the proliferation and migration of cancer cells.PloS one · 2015Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
MicroRNAs (miRs) function primarily as post-transcriptional negative regulators of gene expression through binding to their mRNA targets. Reliable prediction of a miR's targets is a considerable bioinformatic challenge of great importance for inferring the miR's function. Sequence-based prediction algorithms have high false-positive rates, are not in agreement, and are not biological context specific. Here we introduce CoSMic (Context-Specific MicroRNA analysis), an algorithm that combines sequence-based prediction with miR and mRNA expression data. CoSMic differs from existing methods--it identifies miRs that play active roles in the specific biological system of interest and predicts with less false positives their functional targets. We applied CoSMic to search for miRs that regulate the migratory response of human mammary cells to epidermal growth factor (EGF) stimulation. Several such miRs, whose putative targets were significantly enriched by migration processes were identified. We tested three of these miRs experimentally, and showed that they indeed affected the migratory phenotype; we also tested three negative controls. In comparison to other algorithms CoSMic indeed filters out false positives and allows improved identification of context-specific targets. CoSMic can greatly facilitate miR research in general and, in particular, advance our understanding of individual miRs' function in a specific context.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.