In silico analysis of alternative splicing on drug-target gene interactions

Background

This repository contains scripts used to reproduce study published in Ji, Mishra, Davuluri, Scientific Reports, 2020. The aim is to perform a global survey and computational analysis of protein isoforms/splice variants that may affect drug-gene interactions.

Prerequisites

• R (≥ 3.4.3)
• Bioconductor
• Data from DGIDB, Ensembl, BioLIP, TCGA, GTEx

Databases

• The Drug Gene Interaction Database (DGIDB) (http://dgidb.org/) - Interactions TSV, Genes TSV, Drugs TSV
• Ensembl GRCh38.p12/GENCODE v30 BioMart (http://useast.ensembl.org/index.html) - Gene, transcript and protein annotations
• BioLIP protein function database (https://zhanglab.ccmb.med.umich.edu/BioLiP/) - Non-redundant set
• DrugBank, CHEMBL and PDB - for ID mapping and conversion
• TCGA, GTEx expression data from UCSC Xena Browser (https://xena.ucsc.edu/)

File desciption

• isoform_drug_targets.R - major R notebook containing the analysis workflow (summary statistics, multiple alignments)
• expression_tcga_gtex.R - RNA-Seq expression analysis of splice variants as shown in Fig. 7 and 8
• helpers.R - script containing some auxiliary functions to be used in the analysis.

License

The MIT License