TF-eQTL

Data tables and scripts for Transcription factor regulators of eQTL effects across individuals and tissues.

Overview of repository

data_tables/: Data tables organized by analysis
plots/: Plots from manuscript and scripts to generate plots
scripts/: Scripts organized by analysis

Analyses included

Variant sets:

Overlap of >=5% MAF GTEx variants with transcription factor ChIPseq and motif information
Overlap with Caviar fine-mapped credible sets of GTEx eQTLs
Effect size (aFC) calculation for variant-gene pairs

Within-tissue TF-eQTLs:

TF-eQTL interactions discovered with tensorqtl

Cross-tissue TF-eQTLs:

Cross-tissue expression-based TF-eQTL correlations discovered with Spearman correlations
Cross-tissue protein-based TF-eQTL correlations discovered with Spearman correlations

Overlap:

Permutations and calculations for ChIPseq and motif overlap of discovered TF-eQTLs
Regulon gene overlap of discovered TF-eQTL genes
Permutations and calculations for ADASTRA allele-specific TF binding overlap of discovered TF-eQTLs

IRF1 knockdown:

Allele specific expression in an IRF1 knockdown experiment (Brandt et al., 2020)

Gene-by-environment interactions and GWAS:

TF-eQTL overlap with gene-by-environment interactions (Findley et al., 2021)
TF-eQTL overlap with GWAS-eQTL colocalizations (Barbeira et al., 2021)