ArticleNucleic acids research2014
Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data.Scientific reports · 2016Pooled it
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- A comprehensive survey of the approaches for pathway analysis using multi-omics data integration.Briefings in bioinformatics · 2022Review
- Multi-Omics Model Applied to Cancer Genetics.International journal of molecular sciences · 2021Review
- Multi-omics data integration considerations and study design for biological systems and disease.Molecular omics · 2021Review
- Comprehensive analysis of mRNA-level and miRNA-level subpathway activities for identifying robust ovarian cancer prognostic signatures.Journal of cellular and molecular medicine · 2020Article
- Circulating Cell-Free Nucleic Acids as Epigenetic Biomarkers in Precision Medicine.Frontiers in genetics · 2020Review
- Computational Oncology in the Multi-Omics Era: State of the Art.Frontiers in oncology · 2020Review
- Transcriptional Characterization of Stage I Epithelial Ovarian Cancer: A Multicentric Study.Cells · 2019Article
- Topologically inferring active miRNA-mediated subpathways toward precise cancer classification by directed random walk.Molecular oncology · 2019Article
- Establishment and characterisation of a new patient-derived model of myxoid liposarcoma with acquired resistance to trabectedin.British journal of cancer · 2019Article
- TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators.Bioinformatics (Oxford, England) · 2019Article
- A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures.Frontiers in genetics · 2019Article
- Integrated miRNA-mRNA spatial signature for oral squamous cell carcinoma: a prospective profiling study of Narrow Band Imaging guided resection.Scientific reports · 2018Article
- A systems biology approach to investigate the mechanism of action of trabectedin in a model of myelomonocytic leukemia.The pharmacogenomics journal · 2018Article
- Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach.Non-coding RNA · 2017Article
- MICRORNA-AUGMENTED PATHWAYS (mirAP) AND THEIR APPLICATIONS TO PATHWAY ANALYSIS AND DISEASE SUBTYPING.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2017Article
- Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification.Oncotarget · 2016Article
- A data-driven network model of primary myelofibrosis: transcriptional and post-transcriptional alterations in CD34+ cells.Blood cancer journal · 2016Article
- Managing Pancreatic Adenocarcinoma: A Special Focus in MicroRNA Gene Therapy.International journal of molecular sciences · 2016Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The production rate of gene expression data is nothing less than astounding. However, with the benefit of hindsight we can assert that, since we completely ignored the non-coding part of the transcriptome, we spent the last decade to study cell mechanisms having few data in our hands. In this scenario, microRNAs, which are key post-trascriptional regulators, deserve special attention. Given the state of knowledge about their biogenesis, mechanisms of action and the numerous experimentally validated target genes, miRNAs are also gradually appearing in the formal pathway representations such as KEGG and Reactome maps. However, the number of miRNAs annotated in pathway maps are very few and pathway analyses exploiting this new regulatory layer are still lacking. To fill these gaps, we present 'micrographite' a new pipeline to perform topological pathway analysis integrating gene and miRNA expression profiles. Here, micrographite is used to study and dissect the epithelial ovarian cancer gene and miRNA transcriptome defining and validating a new regulatory circuit related to ovarian cancer histotype specificity.
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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.