Last updated: 2018-07-02

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This is my online notebook to document and share the full results of genome-wide enrichment analyses described in the manuscript:

Xiang Zhu and Matthew Stephens (2017). A large-scale genome-wide enrichment analysis identifies new trait-associated genes, pathways and tissues across 31 human phenotypes. bioRxiv.

The software that was used to generate these results is available at Here is an example illustrating how to use this software to perform genome-wide enrichment analyses of GWAS summary statistics.

If you find results shown in this notebook and/or methods implemented in the software useful for your work, please cite the manuscript listed above, Zhu and Stephens (2017).

If you have any question about this notebook or the software, please feel free to contact me: Xiang Zhu, or

Additional resources

  • Where can I find “baseline” model fitting results of all 31 traits?

You can find summary results of “baseline” model fitting at For me, the baseline model fitting results are merely inferential “bases” for the enrichment model fitting results shown in the “Main results” section above. However, when I was presenting the enrichment results during my Ph.D. thesis defense, Prof. John Novembre and Prof. Xin He both pointed out these baseline results might be useful for other on-going projects on the “fourth floor”. Their comments motivated me to create a separate online notebook to share the baseline summary results.

  • Where can I find “Round 1” results of all 3913 pathways?

Currently you need to contact me directly to view our “Round 1” results of all 3913 pathways. When this work was under review, one referee pointed out that our online results, especially our “Round 1” analysis results, were “needlessly complicated” and did not have “any obvious benefit”. Hence, I removed the “Round 1” analysis results from this notebook to simplify the presentation.

  • Where can I find the gene prioritization results?

Currently you need to contact me directly to view our full prioritization results. Unlike the gene set enrichment results, the gene prioritization results cannot be easily tabulated, and thus I have not displayed them in this notebook yet.

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