ArticlePloS one2021
miRGTF-net: Integrative miRNA-gene-TF network analysis reveals key drivers of breast cancer recurrence.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 30 citations in OpenAlex.
- miRSiC: a regulatory-aware machine learning framework for microRNA expression inference across bulk and single-cell transcriptomes.Briefings in bioinformatics · 2026Article
- Regulatory Genetic Networks by microRNAs: Exploring Genomic Signatures in Cervical Cancer.Biomedicines · 2025Review
- Identification of the EBF1/ETS2/KLF2-miR-126-Gene Feed-Forward Loop in Breast Carcinogenesis and Stemness.International journal of molecular sciences · 2025Article
- Predicting the Effect of miRNA on Gene Regulation to Foster Translational Multi-Omics Research-A Review on the Role of Super-Enhancers.Non-coding RNA · 2024Review
- Exploring the Relationship between MicroRNAs, Intratumoral Microbiota, and Breast Cancer Progression in Patients with and without Metastasis.International journal of molecular sciences · 2024Article
- Exploring miRNA‑target gene profiles associated with drug resistance in patients with breast cancer receiving neoadjuvant chemotherapy.Oncology letters · 2024Article
- MIO: microRNA target analysis system for immuno-oncology.Bioinformatics (Oxford, England) · 2022Article
- Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids.Molecular biology and evolution · 2022Article
- Changes in the Expression of miRNA Isoforms and Their Targets in HT-29 Cells after Hypoxic Exposure.Bulletin of experimental biology and medicine · 2022Article
- Expression of CD44 Isoforms in Tumor Samples and Cell Lines of Human Colorectal Cancer.Bulletin of experimental biology and medicine · 2022Article
- A novel approach for a joint analysis of isomiR and mRNA expression data reveals features of isomiR targeting in breast cancer.Frontiers in genetics · 2022Article
- miRModuleNet: Detecting miRNA-mRNA Regulatory Modules.Frontiers in genetics · 2022Article
- Article
- ExhauFS: exhaustive search-based feature selection for classification and survival regression.PeerJ · 2022Article
- Identification of key miRNAs in prostate cancer progression based on miRNA-mRNA network construction.Computational and structural biotechnology journal · 2022Article
- Article
- HIF-DependentFrontiers in genetics · 2021Article
- ECM-Receptor Regulatory Network and Its Prognostic Role in Colorectal Cancer.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of regulatory networks is a powerful framework for identification and quantification of intracellular interactions. We introduce miRGTF-net, a novel tool for construction of miRNA-gene-TF networks. We consider multiple transcriptional and post-transcriptional interaction types, including regulation of gene and miRNA expression by transcription factors, gene silencing by miRNAs, and co-expression of host genes with their intronic miRNAs. The underlying algorithm uses information on experimentally validated interactions as well as integrative miRNA/mRNA expression profiles in a given set of samples. The latter ensures simultaneous tissue-specificity and biological validity of interactions. We applied miRGTF-net to paired miRNA/mRNA-sequencing data of breast cancer samples from The Cancer Genome Atlas (TCGA). Together with topological analysis of the constructed network we showed that considered players can form reliable prognostic gene signatures for ER-positive breast cancer. A number of signatures demonstrated remarkably high accuracy on transcriptomic data obtained by both microarrays and RNA sequencing from several independent patient cohorts. Furthermore, an essential part of prognostic genes were identified as direct targets of transcription factor E2F1. The putative interplay between estrogen receptor alpha and E2F1 was suggested as a potential recurrence factor in patients treated with tamoxifen. Source codes of miRGTF-net are available at GitHub (https://github.com/s-a-nersisyan/miRGTF-net).
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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.