ArticleNucleic acids research2023
GeneFriends: gene co-expression databases and tools for humans and model organisms.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- mGEM: multigraph estimation models for pattern analysis.BMC bioinformatics · 2026Article
- AXOLOTL: an accurate method for detecting aberrant gene expression in rare diseases using coexpression constraints.Bioinformatics (Oxford, England) · 2026Article
- Pleiotropy and disease interactors: the dual nature of genes linking ageing and ageing-related diseases.Biogerontology · 2026Article
- Uncovering coordinated pathway interactions through gene co-differential expression in yeast.Nucleic acids research · 2026Article
- A Multi-level Perspective on the Evolution of Orthologs and Their Functions.Journal of molecular evolution · 2025Review
- SALVE: prediction of interorgan communication with transcriptome latent space representation.American journal of physiology. Heart and circulatory physiology · 2025Article
- LncRNA Foxo6os as a Novel " Scaffold" Mediates MYBPC3 in Combating Pathological Cardiac Hypertrophy and Heart Failure.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Transcriptomic Analysis ofBrain sciences · 2025Article
- Utilizing rat kidney gene co-expression networks to enhance safety assessment biomarker identification and human translation.iScience · 2025Article
- Neutrophil extracellular trap gene expression signatures identify prognostic and targetable signaling axes for inhibiting pancreatic tumour metastasis.Communications biology · 2025Article
- Developing a novel medulloblastoma diagnostic with miRNA biomarkers and machine learning.Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery · 2025Article
- CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders.Nucleic acids research · 2025Article
- A novel clinically relevant antagonistic interplay between prolactin and oncogenic YAP-CCN2 pathways as a differentiation therapeutic target in breast cancer.Cell death & disease · 2025Article
- miRNA-Based Diagnosis of Schizophrenia Using Machine Learning.International journal of molecular sciences · 2025Article
- Clinical relevance of macromolecular complexes involving integrins, potassium and sodium ion channels and the sodium/proton antiporter in human breast cancer.Cancer cell international · 2025Article
- CyExpDB: a web-based multi-species tissue-specific gene expression platform for functional genomics in Cyprinidae fish.Database : the journal of biological databases and curation · 2025Article
- Spermine Synthase : A Potential Prognostic Marker for Lower-Grade Gliomas.Journal of Korean Neurosurgical Society · 2025Article
- GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data.PLoS computational biology · 2025Article
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Authors and funding
8 authors.
Funding
Abstract
Gene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA-seq) data has created opportunities for researchers to employ this abundant data to help decipher the complexity and biology of genomes. Co-expression networks have proven effective for inferring the relationship between the genes, for gene prioritization and for assigning function to poorly annotated genes based on their co-expressed partners. To facilitate such analyses we created previously an online co-expression tool for humans and mice entitled GeneFriends. To continue providing a valuable tool to the scientific community, we have now updated the GeneFriends database and website. Here, we present the new version of GeneFriends, which includes gene and transcript co-expression networks based on RNA-seq data from 46 475 human and 34 322 mouse samples. The new database also encompasses tissue-specific gene co-expression networks for 20 human and 21 mouse tissues, dataset-specific gene co-expression maps based on TCGA and GTEx projects and gene co-expression networks for additional seven model organisms (fruit fly, zebrafish, worm, rat, yeast, cow and chicken). GeneFriends is freely available at http://www.genefriends.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 Socratic graph.