Supplemental Material for Tyler et al. 2019
figureposted on 06.11.2019 by Anna Tyler, J. Matthew Mahoney, Gregory W. Carter
Figures are generally photos, graphs and static images that would be represented in traditional pdf publications.
Fig S1 QQ plots of p values To test for population structure in this patient cohort, we performed marker regression tests for each phenotype using sex as a covariate. We plotted the quantile normalized p values against the theoretical normal distribution. If population structure were affecting the SNP associations, we would expect to see systematic deviation from the line y = x in these plots. Rather we see that the distribution almost perfectly matches the theoretical distribution. The only deviations are a few significant p values in the HLA region for the ACA phenotype. We concluded that there was no population structure in this population and did not use a correction for population structure in our analysis.
Fig S2. Functional enrichment of co-expressed genes We searched across multiple subsets of data sets in the Gene Expression Omnibus (GEO) for genes significantly co-expressed with either RBMS3 and WNT5A or RBMS3 and MSI2. This series of figures reports all terms significantly associated with each pair in each data subset. Bars show the −log10(p) of the enrichment. Blue highlighting indicates a term matching one of the key words we used to identify SSc-related terms.