FarmGTEx TWAS-server

FarmGTEx TWAS-server enables transcriptome-wide association studies (TWAS) across tissues and species using gene expression data from human, pig, and cattle.

Key Features:

• Multispecies gene expression prediction: Provides prediction models for 38,180 human genes, 21,037 pig genes, and 17,942 cattle genes based on expression data from 49 human tissues (838 individuals), 34 pig tissues (5457 individuals), and 23 cattle tissues (4889 individuals).
• GWAS summary statistics imputation: Supports imputation of genome-wide association study summary statistics for downstream analysis.
• Customizable TWAS analysis: Allows users to perform tailored transcriptome-wide association studies across tissues and species.
• Functional annotation: Provides functional interpretation of genetic findings from TWAS analyses.
• Precomputed trait associations: Includes 479,203 tissue-gene-trait associations for 1129 human traits, 1208 associations for 41 cattle traits, and 657 associations for 11 pig traits.

Scientific Applications:

• Cross-species genetic mechanism investigation: Facilitates investigation of molecular mechanisms linking genetic loci to complex phenotypes across human, pig, and cattle.
• Trait-associated gene validation: Enables validation of gene-trait associations, such as the ABCD4 gene with pig teat number.
• Cross-species trait similarity identification: Supports identification of shared genetic similarities between traits across species, such as pig backfat thickness with human diastolic blood pressure, sarcoidosis (Löfgren syndrome), and body mass index.
• Gene expression prediction: Supports genotype-based prediction of gene expression levels for use in association analyses.

Methodology:

The server implements a TWAS analytical pipeline involving construction of gene expression reference panels, gene expression prediction, and association analysis using genome-wide association study data.