An update to GeneFriends, an online microarray- and RNA sequencing-based co-expression database for human and mouse genes and human transcripts, is reported in Nucleic Acids Research this week. Amid the rapid growth of publicly available RNA-seq data, researchers from the University of Liverpool created GeneFriends to facilitate the usage of co-expression networks for inferring the relationship between genes, for gene prioritization, and for assigning function to poorly annotated genes based on their co-expressed partners. They have now updated the tool to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples. The database also now encompasses tissue-specific gene co-expression networks for 20 human and 21 mouse tissues, dataset-specific gene co-expression maps based on The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) projects, and gene co-expression networks for seven additional model organisms: fruit fly, zebrafish, worm, rat, yeast, cow, and chicken. GeneFriends' developers write that they plan to add the tissue-specific networks for TCGA and GTEx in future versions of the database. "We also plan to add cancer-specific co-expression networks for the users interested in comparing networks generated from various cancer-types … to create gender-specific co-expression maps … [and] to generate conserved co-expression network to compare network from different species," they write.
Gene Co-Expression Database for Humans, Model Organisms Gets Update
Dec 02, 2022