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Gene expression across 91 tissues and cell types from 723 RNA-seq datasets in cattle

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LingzhaoFang1/Cattle-GeneAtlas

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Cattle-GeneAtlas

Gene expression (FPKM) across 91 tissues and cell types from 723 RNA-seq datasets in cattle. We computed the t-statistic to measure the tissue-specific expression pattern for each gene in each tissue and cell type. Our cattle-GeneAtlas V1 provides a primary source for GWAS interpretation, functional validation, studies of adaptive evolution, domestication and genomic improvement in livestock. For intance, you could conducted a tissue-enrichment analysis (like GO or KEGG enrichment analysis) using Cattle-GeneAtlas to detect the potential tissues or cell types on which genes of your interest (e.g., from a certain GWAS or evolution study) would act. You also could differentially weight SNPs in genes that are highly specificially expressed in the trait-relevant tissues in the prediction models (like SSGP, multi-BLUP or BayesRC) to improve genomic prediction for that particular trait, especially in the multi-breeds or over-generation situations.

Cattle_GeneAtlas_Expression_Summary_Clustering.R

This R code can be used to explore and plot the number of expressed genes and samples clustering patterns from both PCA and t-SNE approaches

Cattle_GeneAtlas_Tissue_Specific_Genes_Defination.R

This R code were used to detect the tissue-specific genes by computing the t-statistics for each gene in a tissue compared to other tissues that not belonging to the same cetagory

Smaples_Summary.Rdata

This R object contains the metadata for all 723 samples, more details can also be found in our manuscript.

Gene_Expression_Altlas_723_part1-4.Rdata

These R onjects contain gene expression (FPKM) for all 24616 Ensembl genes across 723 samples, based on UMD3.1

outrigger_psi.csv

This file contains the PSI (percent spliced-in) output from outrigger sotfware (https://yeolab.github.io/outrigger/). PSI is for measuring the alternative splcing events.

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