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)