ArticleNucleic acids research2015
GeneFriends: a human RNA-seq-based gene and transcript co-expression database.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
61 citing papers in PubMed.
- Molecular Transducers of Human Skeletal Muscle Remodeling under Different Loading States.Cell reports · 2020Trial
- Integrative Physiological and Transcriptomic Analyses of Oat (Plants (Basel, Switzerland) · 2026Article
- mGEM: multigraph estimation models for pattern analysis.BMC bioinformatics · 2026Article
- Alzheimer's disease polygenic risk score associates with hippocampal subfield atrophy and immune-related genetic mechanism.Frontiers in aging neuroscience · 2026Article
- miRNA-Based Diagnosis of Schizophrenia Using Machine Learning.International journal of molecular sciences · 2025Article
- Exploration of synthesis of anthocyanins in passion fruit pericarp through combinatorial transcriptomic analysis and WGCNA.Frontiers in plant science · 2025Article
- Identification of environment-insensitive genes for oil content by combination of transcriptome and genome-wide association analysis in rapeseed.Biotechnology for biofuels and bioproducts · 2024Article
- FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data.Bioinformatics (Oxford, England) · 2024Article
- CoGTEx: Unscaled system-level coexpression estimation from GTEx data forecast novel functional gene partners.PloS one · 2024Article
- Network Preservation Analysis Reveals Dysregulated Metabolic Pathways in Human Vascular Smooth Muscle Cell Phenotypic Switching.Circulation. Genomic and precision medicine · 2023Article
- FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization.iScience · 2023Article
- GeneFriends: gene co-expression databases and tools for humans and model organisms.Nucleic acids research · 2023Article
- COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.Nucleic acids research · 2023Article
- Gene co-expression analyses of health(span) across multiple species.NAR genomics and bioinformatics · 2022Article
- Dysregulated long non-coding RNA in Sjögren's disease impacts both interferon and adaptive immune responses.RMD open · 2022Article
- Approaches in Gene Coexpression Analysis in Eukaryotes.Biology · 2022Review
- Identification of condition-specific regulatory mechanisms in normal and cancerous human lung tissue.BMC genomics · 2022Article
- New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork.Genes · 2022Article
- Histone Variant macroH2A1.1 Enhances Nonhomologous End Joining-dependent DNA Double-strand-break Repair and Reprogramming Efficiency of Human iPSCs.Stem cells (Dayton, Ohio) · 2022Article
- Kinase-dead mutation: A novel strategy for improving soybean resistance to soybean cyst nematode Heterodera glycines.Molecular plant pathology · 2022Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Co-expression networks have proven effective at assigning putative functions to genes based on the functional annotation of their co-expressed partners, in candidate gene prioritization studies and in improving our understanding of regulatory networks. The growing number of genome resequencing efforts and genome-wide association studies often identify loci containing novel genes and there is a need to infer their functions and interaction partners. To facilitate this we have expanded GeneFriends, an online database that allows users to identify co-expressed genes with one or more user-defined genes. This expansion entails an RNA-seq-based co-expression map that includes genes and transcripts that are not present in the microarray-based co-expression maps, including over 10,000 non-coding RNAs. The results users obtain from GeneFriends include a co-expression network as well as a summary of the functional enrichment among the co-expressed genes. Novel insights can be gathered from this database for different splice variants and ncRNAs, such as microRNAs and lincRNAs. Furthermore, our updated tool allows candidate transcripts to be linked to diseases and processes using a guilt-by-association approach. GeneFriends is freely available from http://www.GeneFriends.org and can be used to quickly identify and rank candidate targets relevant to the process or disease under study.
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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.