ArticleDatabase : the journal of biological databases and curation2015
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse.
Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 301 papers, 2 of them syntheses that pooled it.
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Who cites it
301 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A Multi-Ancestry GWAS Meta-Analysis Integrated with In-Depth Silico, Systems Biology, and Pharmacogenomics Approaches on Alzheimer's Disease Among 1,198,689 Subjects.Journal of molecular neuroscience : MN · 2025Pooled it
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- The role of microRNAs in executive functions: a comprehensive review and bioinformatics analysis of human and animal studies.Molecular psychiatry · 2026Review
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- GRNContext: an interactive web platform for contextualized gene regulatory networks visualization across human cancers.Bioinformatics (Oxford, England) · 2026Article
- IL-6-induced C/EBPα drives follicular regulatory T cell differentiation to regulate humoral immunity in mice.Nature communications · 2026Article
- Unveiling the transcriptomic landscape of coronavirus disease 2019 and psoriasis via systems biology-based analysis.The Journal of international medical research · 2026Article
- Prediction of parsimonious and temporally sensitive sets of cell fate engineering transcription factors with IMCell.bioRxiv : the preprint server for biology · 2026Article
- Shared gene signatures and biochemical regulatory networks linking Parkinson's disease and ulcerative colitis.NPJ Parkinson's disease · 2026Article
- Multiplex networks-based directed graph neural network for cancer driver gene identification.PLoS computational biology · 2026Article
- Targeting PSAT1 in diabetic kidney disease: a ferroptosis-driven strategy for precision therapy.Molecular and cellular biochemistry · 2026Article
- PSGRN: Gene regulatory network inference from single-cell perturbational data through self-training with synthetic gold standards.Science advances · 2026Article
- An integrated analysis of lactylation signature reveals PRDX1 as a therapeutic target of keloid pathogenesis.Scientific reports · 2026Article
- SC-MO-GRN-DB: A comprehensive repository for single-cell multiomic gene regulatory networks.iScience · 2026Article
- AutoGERN: single-cell RNA-seq gene regulatory network inference via explicit link modeling and adaptive architectures.Bioinformatics (Oxford, England) · 2026Article
- Identification of a Novel Mitochondrial-Related Gene Signature for BMSCs in Osteoporosis Combining Single-Cell and Bulk Transcriptome Data.Biochemical genetics · 2026Article
- GCNPath: introspecting drug response prediction with pathway-guided graph convolution networks.Communications biology · 2026Article
- Differential microRNA expression profiles and predicted miRNA-mRNA regulatory networks in human macrophage-like cells infected with Leishmania infantum.Scientific reports · 2026Article
- Identification and bioinformatic functional analysis of novel and known polymorphisms in the myostatin gene of Ukrainian Carpathian Mountain sheep.Scientific reports · 2026Article
241 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Transcriptional and post-transcriptional regulation of gene expression is of fundamental importance to numerous biological processes. Nowadays, an increasing amount of gene regulatory relationships have been documented in various databases and literature. However, to more efficiently exploit such knowledge for biomedical research and applications, it is necessary to construct a genome-wide regulatory network database to integrate the information on gene regulatory relationships that are widely scattered in many different places. Therefore, in this work, we build a knowledge-based database, named 'RegNetwork', of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among transcription factors (TFs), microRNAs (miRNAs) and target genes from 25 selected databases. Moreover, we also inferred and incorporated potential regulatory relationships based on transcription factor binding site (TFBS) motifs into RegNetwork. As a result, RegNetwork contains a comprehensive set of experimentally observed or predicted transcriptional and post-transcriptional regulatory relationships, and the database framework is flexibly designed for potential extensions to include gene regulatory networks for other organisms in the future. Based on RegNetwork, we characterized the statistical and topological properties of genome-wide regulatory networks for human and mouse, we also extracted and interpreted simple yet important network motifs that involve the interplays between TF-miRNA and their targets. In summary, RegNetwork provides an integrated resource on the prior information for gene regulatory relationships, and it enables us to further investigate context-specific transcriptional and post-transcriptional regulatory interactions based on domain-specific experimental data. Database URL: http://www.regnetworkweb.org.
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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.