GeneFriends: gene co-expression databases and tools for humans and model organisms. Issue Volume 51:Issue D1(2023) (1st December 2022)

• Record Type: Journal Article
• Authors: Raina, Priyanka; Guinea, Rodrigo; Chatsirisupachai, Kasit; Lopes, Inês; Farooq, Zoya; Guinea, Cristina; Solyom, Csaba-Attila; de Magalhães, João Pedro
• Is Part Of: Nucleic acids research. Volume 51:Issue D1(2023)
• Page Start: D145
• Page End: D158
• Publication Date: 2022-12-01
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac1031
• Languages: English
• ISSNs: 0305-1048

Abstract

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/ .