ArticleBioinformatics (Oxford, England)2016
Integrated gene set analysis for microRNA studies.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- MicroRNA, Myostatin, and Metabolic Rate Depression: Skeletal Muscle Atrophy Resistance in HibernatingCells · 2024Article
- Reduced Levels of miR-145-3p Drive Cell Cycle Progression in Advanced High-Grade Serous Ovarian Cancer.Cells · 2024Article
- Hibernation-Induced microRNA Expression Promotes Signaling Pathways and Cell Cycle Dysregulation inMetabolites · 2023Article
- Plasma Extracellular Vesicles Play a Role in Immune System Modulation in Minimal Hepatic Encephalopathy.International journal of molecular sciences · 2022Article
- PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases.Nucleic acids research · 2022Article
- Identification of Novel microRNA Profiles Dysregulated in Plasma and Tissue of Abdominal Aortic Aneurysm Patients.International journal of molecular sciences · 2020Article
- Lack of TLR4 modifies the miRNAs profile and attenuates inflammatory signaling pathways.PloS one · 2020Article
- Identification of two microRNA nodes as potential cooperative modulators of liver metabolism.Hepatology research : the official journal of the Japan Society of Hepatology · 2019Article
- Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex.Scientific reports · 2018Article
- A Filtering Method for Identification of Significant Target mRNAs of Coexpressed and Differentially Expressed MicroRNA Clusters.Journal of healthcare engineering · 2018Article
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- BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets.BMC bioinformatics · 2017Article
- MicroRNA profiling associated with non-small cell lung cancer: next generation sequencing detection, experimental validation, and prognostic value.Oncotarget · 2017Article
- Asthma remission: Predicting future airways responsiveness using an miRNA network.The Journal of allergy and clinical immunology · 2017Article
- QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing.BMC bioinformatics · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationFunctional interpretation of miRNA expression data is currently done in a three step procedure: select differentially expressed miRNAs, find their target genes, and carry out gene set overrepresentation analysis Nevertheless, major limitations of this approach have already been described at the gene level, while some newer arise in the miRNA scenario.Here, we propose an enhanced methodology that builds on the well-established gene set analysis paradigm. Evidence for differential expression at the miRNA level is transferred to a gene differential inhibition score which is easily interpretable in terms of gene sets or pathways. Such transferred indexes account for the additive effect of several miRNAs targeting the same gene, and also incorporate cancellation effects between cases and controls. Together, these two desirable characteristics allow for more accurate modeling of regulatory processes.
resultsWe analyze high-throughput sequencing data from 20 different cancer types and provide exhaustive reports of gene and Gene Ontology-term deregulation by miRNA action. AVAILABILITY AND IMPLEMENTATION: The proposed methodology was implemented in the Bioconductor library mdgsa http://bioconductor.org/packages/mdgsa For the purpose of reproducibility all of the scripts are available at https://github.com/dmontaner-papers/gsa4mirna CONTACT: : david.montaner@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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