Omics SMR plot

A web-based tool to generate omics SMR plots (see the example below). Citation: Wu et al. (2018) Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits. Nature Communications, 9: 918.
Please input a value > 0 and < 1
Please input a value > 0 and < 1
Please input a number

Optional flags


Credits: Zhili Zheng, Yang Wu, Zhihong Zhu, Futao Zhang, Ting Qi and Jian Yang at the Program in Complex Trait Genomics, The University of Queensland

Troubleshooting: Zhili Zheng or Jian Yang

SMR command line to generate the data file for plot
#Run the following command on your local computer
smr --bfile mydata --gwas-summary mygwas.ma --beqtl-summary mymqtl --beqtl-summary myeqtl --out myplot --plot --probe ILMN_123 --probe-wind 500 --gene-list glist-hg19

See SMR website for details of the flags. You can speed up the uploading by compressing the output file in zip format. Note that all the uploaded data will be deleted after finishing the plot.

Demo data


Notes
eSMR threshold To specify the genome-wide significance threshold used in the SMR test for association between gene expression and trait.
mSMR threshold To specify the genome-wide significance threshold used in the SMR test for association between DNA methylation and trait.
Window size To set the size of a window centred around the focal probe (or the user-specified centre position; see flag below) to generate the plot.
Trait name To specify the name of the trait or disease displayed on the GWAS plot.
Highlight a SNP To specify a SNP to highlight on the GWAS plot.
m2eSMR threshold To specify the threshold used in the SMR test for association between DNA methylation and gene expression.
eSMR HEIDI threshold To specify the threshold used in the HEIDI test for association between gene expression and trait.
mSMR HEIDI threshold To specify the threshold used in the HEIDI test for association between DNA methylation and trait.
m2eSMR HEIDI threshold To specify the threshold used in the HEIDI test for association between DNA methylation and gene expression.
Plot centre position To specify the centre physical position of the plot.
Max No. mQTL plots To specify the maximum number of mQTL plots.
mQTL plots To specify user-defined mQTL plot(s).
eQTL plots To specify user-defined eQTL plot(s).
Max No. labelled probe names To specify the maximum number of probes labelled on the top panel of the plot.
Label the methylation probes To label the DNA methylation probes on the top panel of the plot.
Label probes passing both SMR and HEIDI only To label only the probes that passed both the SMR and HEIDI tests on the top panel of the plot.
Plot Roadmap epigenomics annotation To plot the Roadmap epigenome annotations (Roadmap Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes (2015) Nature 518, 317–330).