ArticleGenome biology2021
GeneWalk identifies relevant gene functions for a biological context using network representation learning.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Rencofilstat, a cyclophilin inhibitor: A phase 2a, multicenter, single-blind, placebo-controlled study in F2/F3 NASH.Hepatology communications · 2022Trial
- Clinico-histopathologic and single-nuclei RNA-sequencing insights into cardiac injury and microthrombi in critical COVID-19.JCI insight · 2022Trial
- Enhancing link prediction in biomedical knowledge graphs with BioPathNet.Nature biomedical engineering · 2026Article
- Article
- An Introduction to Network Analysis in Plant Biology.Plant direct · 2025Article
- Functional dissection of noncoding variants associated with rheumatoid arthritis.Annals of the rheumatic diseases · 2025Article
- Protective exercise responses in the dentate gyrus of Alzheimer's disease mouse model revealed with single-nucleus RNA-sequencing.Nature neuroscience · 2025Article
- Identification of Prognostic Biomarkers in Gene Expression Profile of Neuroblastoma Via Machine Learning.Pediatric discovery · 2025Article
- GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data.PLoS computational biology · 2025Article
- Graph contrastive learning of subcellular-resolution spatial transcriptomics improves cell type annotation and reveals critical molecular pathways.Briefings in bioinformatics · 2024Article
- A best-match approach for gene set analyses in embedding spaces.Genome research · 2024Article
- Unveiling hidden connections in omics data via pyPARAGON: an integrative hybrid approach for disease network construction.Briefings in bioinformatics · 2024Article
- Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.Molecular cell · 2024Article
- Sex-biasing influence of autism-associatedScience advances · 2024Article
- Early-stage lung cancer is driven by a transitional cell state dependent on a KRAS-ITGA3-SRC axis.The EMBO journal · 2024Article
- SIMBA: single-cell embedding along with features.Nature methods · 2024Article
- From tradition to innovation: conventional and deep learning frameworks in genome annotation.Briefings in bioinformatics · 2024Review
- Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns.Biology methods & protocols · 2024Article
- Current and future directions in network biology.Bioinformatics advances · 2024Article
- Explainable Multilayer Graph Neural Network for cancer gene prediction.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
A bottleneck in high-throughput functional genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Gene Ontology (GO) enrichment methods provide insight at the gene set level. Here, we introduce GeneWalk ( github.com/churchmanlab/genewalk ) that identifies individual genes and their relevant functions critical for the experimental setting under examination. After the automatic assembly of an experiment-specific gene regulatory network, GeneWalk uses representation learning to quantify the similarity between vector representations of each gene and its GO annotations, yielding annotation significance scores that reflect the experimental context. By performing gene- and condition-specific functional analysis, GeneWalk converts a list of genes into data-driven hypotheses.
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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.