We here uniformly analyzed 723 (156 newly generated and 567 existing) RNA-seq datasets to build a gene atlas in cattle, which included 91 tissues and cell types from 447 individuals. We summarized the sample information, their NCBI accession numbers, and expression (FPKM) of 24,616 Ensembl genes (based on UMD3.1) here. Through integrative analyses of this gene atlas with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle (under review in Genome Research). This cattle gene atlas will serve as a primary source for biological interpretation and functional validation of GWAS findings, studies of adaptive evolution and population genetics, as well as genomic improvement in cattle.
This page allows the user to search for the expression of genes of interest based on Ensembl gene ID or gene symbol, and plot them according to tissue types. It also allows the user to do phenome-wide association analysis (pheWAS) for genes of interest in UK Biobank in humans by querying the GeneAtlas website. The annotation of orthologues genes between human and cattle was from Ensembl version 94. The results could be downloaded freely.
Now this work is published in Genome Research. Please, cite it if you find this data useful.