{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T00:59:52Z","timestamp":1791593992953,"version":"4.3.4"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,12,1]],"date-time":"2022-12-01T00:00:00Z","timestamp":1669852800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["208375\/Z\/17\/Z"],"award-info":[{"award-number":["208375\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/R014949\/1"],"award-info":[{"award-number":["BB\/R014949\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004156","name":"Mahidol University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004156","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000836","name":"University of Liverpool","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000836","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"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>","DOI":"10.1093\/nar\/gkac1031","type":"journal-article","created":{"date-parts":[[2022,12,1]],"date-time":"2022-12-01T17:55:02Z","timestamp":1669917302000},"page":"D145-D158","source":"Crossref","is-referenced-by-count":51,"title":["GeneFriends: gene co-expression databases and tools for humans and model organisms"],"prefix":"10.1093","volume":"51","author":[{"given":"Priyanka","family":"Raina","sequence":"first","affiliation":[{"name":"Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool , Liverpool \u00a0L7 8TX, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodrigo","family":"Guinea","sequence":"additional","affiliation":[{"name":"Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool , Liverpool \u00a0L7 8TX, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kasit","family":"Chatsirisupachai","sequence":"additional","affiliation":[{"name":"Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool , Liverpool \u00a0L7 8TX, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"In\u00eas","family":"Lopes","sequence":"additional","affiliation":[{"name":"Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool , Liverpool \u00a0L7 8TX, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zoya","family":"Farooq","sequence":"additional","affiliation":[{"name":"Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool , Liverpool \u00a0L7 8TX, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"Guinea","sequence":"additional","affiliation":[{"name":"UCAL - Universidad de Ciencias y Artes de Am\u00e9rica Latina, Faculty of Design , Lima \u00a015026, Per\u00fa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Csaba-Attila","family":"Solyom","sequence":"additional","affiliation":[{"name":"Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool , Liverpool \u00a0L7 8TX, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6363-2465","authenticated-orcid":false,"given":"Jo\u00e3o Pedro","family":"de\u00a0Magalh\u00e3es","sequence":"additional","affiliation":[{"name":"Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool , Liverpool \u00a0L7 8TX, UK"},{"name":"Institute of Inflammation and Ageing, University of Birmingham, Queen Elizabeth Hospital, Mindelsohn Way , Birmingham \u00a0B15 2WB, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,1]]},"reference":[{"key":"2023010804280299700_B1","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1101\/gr.5145806","article-title":"Gene discovery and annotation using LCM-454 transcriptome sequencing","volume":"17","author":"Emrich","year":"2007","journal-title":"Genome Res."},{"key":"2023010804280299700_B2","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.cell.2008.03.029","article-title":"Highly integrated single-base resolution maps of the epigenome in arabidopsis","volume":"133","author":"Lister","year":"2008","journal-title":"Cell"},{"key":"2023010804280299700_B3","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nrg2934","article-title":"RNA sequencing: advances, challenges and opportunities","volume":"12","author":"Ozsolak","year":"2011","journal-title":"Nat. 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