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Additional file 1. Appendix

Additional file 3: Table S3. GR methylation in U and C regions for patients by outcome.

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Additional file 2. Supplemental Table 2: DEPICT genetic association in pathways.

Additional file 12: Table S1. Total number of ones, zeros and nulls in the sparse matrix for the 163 TFs used in this study.

Additional optimization code (MATLAB). (TXT 2Â kb)

Additional file7: Table S18. DNAmeQTL analysis for the loci significantly associated with DNAme-based XCI status calls. See additional files. These loci were independently tested as DNAmeQTLs in females and males, with some columns color coded based on sex (pink female, light blue male). There are also columns with the median and mean DNAme value at the gene’s island for samples with the reference or alternate allele at that loci; these columns are color coded based on whether the allele is in the range to escape from XCI (DNAme<0.01, blue) or in the range to be subject to XCI (DNAme>0.15, orange). There are mean and median columns for both males and females, but only the female columns are color coded based on XCI status. There are boxes around the genes with female median values with one allele in the range to escape XCI and the other allele in the range to be subject to XCI.