This repository contains scripts, data, results, figures and reproducibility report for "ADH and ALDH gene regulation" study. In this study, we identified all eQTL SNPs that are involved in ADH and ALDH gene regulation and explored whether they are associated with alcohol dependence, psychiatric disorders and cognition.
Python (version 3.6.9), R (version 4.0.2) and RStudio (version 1.2.5033) were used for data processing, analysis and visualisation.
- Cell type- and tissue-specific Hi-C data is available on GEO or ENCODE databases (Accessions: GSE77565, GSE105194, GSE105513, GSE105544, GSE105914, GSE52457, GSE105957, GSE35156, GSE43070, GSE35156, GSE43070, GSE63525, GSE105235, GSE105275, GSE105318, GSE105465, GSE105491, GSE105556, GSE105557, GSE105566, GSE105600, GSE105697, GSE105710, GSE105725, GSE105988, GSE106015, GSE106022, GSE92819, GSE126199, GSE105381, ENCSR504OTV, ENCSR479USL, GSE134761, GSE115491, GSE122958, GSE105776, GSE98161, GSE87112, ENCSR748LQF).
- RNA-seq and genotyping data (GTEx v8) are available via dbGaP access (phs000424.v8.p2).
- Human genome build hg38 release 75 (GRCh38) (Homo_sapiens_assembly38_noALT_noHLA_noDecoy.fasta) was downloaded from gs://gtex-resources.
- SNP genomic positions for genome GRCh38p7 build 151 were obtained from the dbSNP ftp site.
- Gene annotations for GENCODE v26 (gencode.v26.GRCh38.genes.gtf) were downloaded from gs://gtex-resources.
ALDH2 eQTLs associated with bipolar disorder, schizophrenia and cognition are involved in brain-specific trans-interchromosomal upregulatory interactions.