Resources

Web server

CattleGTEx Atlas

A multi-tissue atlas of regulatory variants in cattle (cis-eQTL, cis-sQTL, trans-eQTL, and trans-sQTL across 23 distinct tissues)


PigGTEx Atlas

A compendium of genetic regulatory effects across pig tissues (cis-eQTL, cis-sQTL, cis-eeQTL, cis-lncQTL, cis-enQTL, bieQTL, and cieQTL)


PigBiobank

A database for understanding the genetics of complex traits in an integrative genomics way. It currently displays results from GWAS, TWAS, colocalization, and Mendelian randomization (MR) of 268 complex traits in pig.


PGPR(Pig Genomics Reference Panel) (under construction)

A free online platform for genotype imputation in pigs.


FarmGTEx TWAS-Server

A free online platform for predicting molecular phenotypes collected in the FarmGTEx and conducting TWAS analysis in farm animals.


ChickenGTEx Atlas

A comprehensive public catalogue of genetic regulatory variants associated with multiple types of transcriptomic phenotypes in distinct biological contexts (e.g., tissues, cell types, development periods, gender, environmental exposures, and genetic backgrounds) in chicken.


SheepGTEx

GoatGTEx

DuckGTEx

...

Open-Access Data

CattleGTEx

  • Exon Junctions
  • Full summary statisitcs (cis-eQTLs)
  • Full summary statisitcs (cis-sQTLs)
  • Gene expression (TPM)
  • Gene read counts
  • Metadata
  • Trans-eQTL
  • Trans-sQTL
  • TWAS Elastic Net model
  • TWAS results
  • Colocalization Plots


PigGTEx

  • (cis-eQTL) Top associations for each protein-coding gene based on permutation mode.
  • (cis-eQTL) Summary statisitcs of significant variant-gene associations for each tissue.
  • (cis-eeQTL) Top associations for each exon based on permutation mode.
  • (cis-eeQTL) Summary statisits of significant variant-exon associations for each tissue.
  • (cis-sQTL) Top associations for each splicing gene based on permutation mode.
  • (cis-sQTL) Summary statisitcs of significant variant-splicing event associations for each tissue.
  • (cis-IncQTL) Top associations for each IncRNA based on permutation mode.
  • (cis-IncQTL) Summary statisitcs of significant variant-IncRNA associations for each tissue.
  • (cis-enQTL) Top associations for each enhancer based on permutation mode.
  • (cis-enQTL) Summary statisits of significant variant-enhancer associations for each tissue.
  • (cis-bieQTL) Top associations of breed interaction eQTL (genotype × breed ancestry).
  • (cieQTL) Top associations of cell type interaction eQTL (genotype × cell type enrichment).
  • Genotype files used for molQTL mapping across 34 pig tissues (Plink v1.9 binary format).
  • Gene annotation of Sscrofa11.1 (v100).
  • Gene expression (TPM) matrix for 34 tissues.
  • Exon expression (TPM) matrix for 34 tissues.
  • LncRNA expression (TPM) matrix for 34 tissues.
  • Enhancer expression (TPM) matrix for 34 tissues.
  • Normalized alternative splicing values (Percent Spliced In, PSI) for 34 tissues.


ChickenGTEx

SheepGTEx

GoatGTEx

DuckGTEx

...

Conferences/Siminars/Workshops

The coming FarmGTEx workshops and siminars will be updated here.




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