GRNContext: An Interactive Web Platform for Contextualized Gene Regulatory Networks Visualization Across Human Cancers

Clicks: 1
ID: 317367
2026
Free PDF
Article Quality & Performance Metrics
Overall Quality
Not rated
Combines reader engagement with the AI quality analysis. This article has not been analysed, so there is no overall score — reader engagement is measured and shown alongside.
AI Quality Assessment
Not analyzed
Readership in this journal

Ranked #808 of 829 articles by views in BMC Bioinformatics

Most read Least read

Bar heights use a square-root scale. Only the 120 most-read articles are drawn; the journal has 829 in total.

Mint this article as an NFT
Not yet minted

Create a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.

5 SUSD one-off · no wallet required
Sign in to mint
Abstract
SUMMARY: While current Gene Regulatory Network (GRN) databases provide comprehensive reference maps of potential interactions between transcription factors and target genes, they do not specify which regulatory interactions are active within specific biological contexts. This limitation is particularly critical in cancer, where transcriptional programs are inherently tissue-specific. To address this gap, we developed GRNContext, an interactive web platform designed for the visualization, exploration, and comparative analysis of gene regulatory networks contextualized across 33 cancer types from The Cancer Genome Atlas (TCGA). Our approach uses the TFLink human reference GRN as a starting point and integrates TCGA transcriptomic profiles to infer cancer-specific regulatory activity. Regulatory relevance was assessed using complementary machine learning and statistical methods, which were unified into a consensus score to prioritize and filter the most relevant candidate regulators for each target gene. By providing both curated context-specific GRNs and a user-friendly platform, GRNContext constitutes a comprehensive and accessible resource that supports mechanistic investigations, hypothesis generation, and translational research focused on transcriptional regulation in cancer. AVAILABILITY AND IMPLEMENTATION: GRNContext is supported by all major browsers and freely available on the web at https://apps.cienciavida.org/grncontext. It is implemented as a client-server web application featuring a FastAPI backend and a React frontend utilizing Cytoscape.js for interactive network visualization, all containerized via Docker for cross-platform compatibility. SUPPLEMENTARY INFORMATION: The source code, supplementary materials, and resources for the GRNContext web platform are accessible at https://doi.org/10.5281/zenodo.18355998..
Reference Key
openalex_W7164818098 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Ignacio Pezoa-Soto, Sergio Hernández-Galaz, Javier de las Rivas, Álvaro Lladser, Manuel Varas-Godoy, Alberto J M Martin
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag389
URL
https://doi.org/10.1093/bioinformatics/btag389
Keywords Keywords not found

Citations

No citations found. To add a citation, contact the admin at info@scimatic.org

Comments

No comments yet. Be the first to comment on this article.