GeneFriends: gene co-expression databases and tools for humans and model organisms

Raina, Priyanka, Guinea, Rodrigo, Chatsirisupachai, Kasit, Lopes, Ines, Farooq, Zoya, Guinea, Cristina, Solyom, Csaba-Attila and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2022) GeneFriends: gene co-expression databases and tools for humans and model organisms. NUCLEIC ACIDS RESEARCH, 51 (D1). D145-D158.

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Official URL: http://dx.doi.org/10.1093/nar/gkac1031

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/.

Item Type:	Article
Uncontrolled Keywords:	Animals, Humans, RNA, Gene Expression Profiling, Sequence Analysis, RNA, Databases, Genetic, Gene Regulatory Networks
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Life Courses and Medical Sciences
Depositing User:	Symplectic Admin
Date Deposited:	07 Feb 2023 09:43
Last Modified:	07 Feb 2023 09:43
DOI:	10.1093/nar/gkac1031
Open Access URL:	https://doi.org/10.1093/nar/gkac1031
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3168233