De novo identification of complex multimorbid conditions by integration of gene regulation and protein interaction networks with genome-wide association studies
This repository contains scripts, data files and results for the manuscript "De novo identification of complex multimorbid conditions by integration of gene regulation and protein interaction networks with genome-wide association studies". In this study, a whole blood-specific spatial gene regulatory network incorporating information about the 3D topology of the genome was constructed. This was combined with data from the GWAS Catalog to identify traits that are proximal to asthma within the constructed regulatory space. This not only allowed for the identification of conditions that are multimorbid with asthma, but also identified the variants and genes that connect asthma and the multimorbid conditions. We demonstrate the applicability of this approach to other complex traits of interest such as acute lymphoblastic leukemia.
Clone the repository using the following command:
git clone https://github.com/Genome3d/asthma_multimorbidities
cd asthma_multimorbidities/
The below package versions were used in this study
STRINGdb 2.2.2, tidyverse 1.3.0., ggrepel 0.8.2, vroom 1.2.1, reshape2 1.4.4, scales 1.1.1, Hmisc 4.4-0, gprofiler2 0.1.9, eulerr 6.1.0, ggpubr 0.3.0, stringr 1.4.0, pheatmap 1.0.12, gplots 3.0.3, gdata 2.18.0, dplyr 1.0.0, plyr 1.8.6, RColorBrewer 1.1-2, biomaRt 2.46.3.
R version 4.0.1 and RStudio version 1.3.959 were used for data processing, analysis and visualisation.
This project is licensed under the MIT License.