{"doi":"10.1093/nar/gkac1031","title":"GeneFriends: gene co-expression databases and tools for humans and model organisms","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>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/.</jats:p>","journal":"Nucleic Acids Research","year":2023,"id":631346,"datarank":0.5983476069846413,"base_score":3.9889840465642745,"endowment":3.9889840465642745,"self_citation_contribution":0.5983476069846413,"citation_network_contribution":0.0,"self_endowment_contribution":0.5983476069846413,"citer_contribution":0.0,"corpus_percentile":67.2,"corpus_rank":4405,"citation_count":53,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1636082,"name":"Rodrigo Guinea","orcid":null,"position":1,"is_corresponding":false},{"id":1609508,"name":"Kasit Chatsirisupachai","orcid":null,"position":2,"is_corresponding":false},{"id":810813,"name":"Inês Lopes","orcid":null,"position":3,"is_corresponding":false},{"id":1636083,"name":"Zoya Farooq","orcid":null,"position":4,"is_corresponding":false},{"id":1636085,"name":"Cristina Guinea","orcid":null,"position":5,"is_corresponding":false},{"id":1636087,"name":"Csaba-Attila Solyom","orcid":null,"position":6,"is_corresponding":false},{"id":5938,"name":"João Pedro de Magalhães","orcid":"0000-0002-6363-2465","position":7,"is_corresponding":false},{"id":1636081,"name":"Priyanka Raina","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"GeneFriends: gene co-expression databases and tools for humans and model organisms","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>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/.</jats:p>","is_dataset_classified":null,"base_score":3.9889840465642745,"endowment":3.9889840465642745,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"36454018","pmcid":"PMC9825523","openalex_id":"https://openalex.org/W4310564850","authors":[],"funders":[{"funder_name":"Wellcome Trust","grant_id":"208375/Z/17/Z","title":null},{"funder_name":"BBSRC","grant_id":"BB/R014949/1","title":"The Human Ageing Genomic Resources"},{"funder_name":"Wellcome Trust","grant_id":"208375","title":"GeneFriends: A gene and transcript co-expression resource"},{"funder_name":"University of Liverpool","grant_id":"","title":null},{"funder_name":"Mahidol University","grant_id":"","title":null},{"funder_name":"Wellcome Trust","grant_id":"","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"","title":null},{"funder_name":"Wellcome Trust","grant_id":"","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"","title":null}],"total_grants":9,"fwci":3.5287,"citation_percentile":0.94487588,"influential_citations":0,"citation_trend":[{"year":2022,"count":1},{"year":2023,"count":10},{"year":2024,"count":14},{"year":2025,"count":20},{"year":2026,"count":8}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/51/D1/D145/48441004/gkac1031.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/51/D1/D145/48441004/gkac1031.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkac1031","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/36454018","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825523","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC9825523","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC9825523?pdf=render","host_type":"Europe_PMC"},{"url":"https://dx.doi.org/10.60692/2wsmp-7jm07","host_type":""},{"url":"https://dx.doi.org/10.60692/rc23p-40394","host_type":""},{"url":"http://dx.doi.org/10.1093/nar/gkac1031","host_type":""}],"fields_of_study":["Bioinformatics and Genomic Networks","RNA Research and Splicing","CRISPR and Genetic Engineering","0301 basic medicine","03 medical and health sciences","0303 health sciences","Animals","Humans","Databases, Genetic","Gene Expression Profiling","Gene Regulatory Networks","RNA","Sequence Analysis, RNA"],"mesh_terms":["Animals","Humans","RNA","Sequence Analysis, RNA","Gene Expression Profiling","Databases, Genetic","Gene Regulatory Networks"],"keywords":["Biology","Gene","Gene expression","Computational biology","Function (biology)","Model organism","Database","Regulation of gene expression","Gene nomenclature","RNA-Seq","Genetics","DECIPHER","Gene regulatory network","Genome","Gene expression profiling","Transcriptome","Computer science","Gene Set Enrichment Analysis","Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins","Biochemistry, Genetics and Molecular Biology","Databases, Genetic","Database Issue","Animals","Humans","Gene Regulatory Networks","Molecular Biology","Gene Editing","Sequence Analysis, RNA","Nomenclature","Co-expression Networks","Botany","Life Sciences","Taxonomy (biology)","Analysis of Gene Interaction Networks","FOS: Biological sciences","Regulation of RNA Processing and Function","RNA"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Partnerships for the goals"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-05T23:23:36.626998Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}