Last updated: 2020-11-30

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Overview

This is my online notebook to document and share the full results of whole-genome integrated analyses of 38 gene regulatory networks and 18 human complex traits described in the following research article:

Xiang Zhu, Zhana Duren, Wing Hung Wong (2020). Modeling regulatory network topology improves genome-wide analyses of complex human traits. bioRxiv. https://doi.org/10.1101/2020.03.13.990010.

If you find the analysis results, the pre-processed networks, the statistical methods, and/or the open-source software useful for your work, please kindly cite the research article listed above (Zhu et al, 2020).

If you have any question about the notebook and/or the article, please feel free to contact me xiangzhu[at]psu.edu.

Main results

For each phenotype below, please click to view network enrichment results, click to view gene prioritization results, and click to view gene cross-reference results. Please note that loading gene prioritization results may take a while because of the large number of genes displayed.

Phenotype (GWAS publication) Network enrichment Gene prioritization Cross reference
Adult height (Wood et al. 2014) N/A
Body mass index (Locke et al. 2015)
Waist-to-hip ratio (Shungin et al. 2015)
Breast cancer (Michailidou et al. 2013)
Rheumatoid arthritis (Okada et al. 2014)
Crohn’s disease (Liu et al. 2015) N/A
Inflammatory bowel disease (Liu et al. 2015)
Ulcerative colitis (Liu et al. 2015)
High-density lipoprotein (Teslovich et al. 2010)
Low-density lipoprotein (Teslovich et al. 2010)
Type 2 diabetes (Morris et al. 2012)
Heart rate (den Hoed et al. 2013)
Coronary artery disease (Nikpay et al. 2015)
Myocardial infarction (Nikpay et al. 2015)
Atrial fibrillation (Christophersen et al. 2017)
Alzheimer’s disease (Lambert et al. 2013)
Schizophrenia (Ripke et al. 2014)
Neuroticism (Okbay et al. 2016)

Additional resources

Icons used in this notebook are credited to the Noun Project. This notebook is created using workflowr. 


devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       Ubuntu 20.04.1 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/New_York            
 date     2020-11-30                  

─ Packages ───────────────────────────────────────────────────────────────────
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 yaml          2.2.1   2020-02-01 [3] CRAN (R 4.0.0)

[1] /home/maimaizhu/R/x86_64-pc-linux-gnu-library/4.0
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library