Additional file 1: of Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

Additional file containing all Additional file 1: Figures S1–S10 and Table S2. (PDF 1142 kb

Additional file 2: of Stochastic epigenetic outliers can define field defects in cancer

GSEA result tables of hypervariable DVCs, as identified using iEVORA, in the normal breast study comparing normal breast from healthy women to normal breast adjacent to breast cancer. There are 4 tables, corresponding to hypervariable DVCs mapping to TSS1500, TSS200 or 1st Exon regions, and which are hypermethylated (dvUPdmUP) or hypomethylated (dvUPdmDN) in normal-adjacent tissue, as well as hypervariable DVCs mapping to gene-body or 5′UTR regions, which are hypermethylated (dvUPdmUP-GB) or hypomethylated (dvUPdmDN-GB) in normal-adjacent tissue. In each case, the columns label the number of genes in the MSigDB database list (nList), the number present prior to iEVORA analysis (nRep), the corresponding fraction (fRep), the number of genes overlapping with the iEVORA selected list (nOVLAP), the corresponding odds ratio (OR) and one-tailed Fisher test P-value (P-value), the adjusted P-value using Benjamini-Hochberg correction, and the gene symbols of the genes present in the overlap. (XLS 54 kb

Additional file 1: of A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies

Contains all Supplementary Figures and Supplementary Tables plus their captions: Figure S1. Clustering validation of reference blood database. Figure S2. Validation of EpiDISH. Figure S3. Improvement of inference using DHS data in 3 independent data sets. Figure S4. Comparison of reference-based methods. Figure S5. Comparative performance of reference-based methods in an EWAS of smoking. Table S1. The blood reference database. Table S2. Gold-standard list of 62 smoking-associated DMCs (sDMCs). Table S3. Smoking-associated DMCs with no adjustment for cell-type composition. Table S4. Smoking-associated DMCs as obtained using EpiDISH. (PDF 1241 kb

Additional file 2: of A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies

An R-script implementing EpiDISH with either robust partial correlations (RPC), CIBERSORT (CBS) or Constrained Projection (CP). (R 5 kb

MOESM2 of Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer

Additional file 2. Pdf document containing all Supplementary Figures S1–11, as well as Supplementary Table S2

Additional file 2 of Tensorial blind source separation for improved analysis of multi-omic data

A file containing R scripts for the tPCA, tWFOBI, tWJADE, CCA, sCCA, PARAFAC, JIVE and iCLUSTER algorithms as implemented in this work. (R 17 kb

Additional file 1 of Tensorial blind source separation for improved analysis of multi-omic data

Contains all supplementary figures and supplementary tables. (DOCX 14322 kb

Additional file 1: of The multi-omic landscape of transcription factor inactivation in cancer

This document contains all Supplementary Tables and all Supplementary Figures, plus their associated legends/captions. (PDF 3658 kb

Additional file 3: of Correlation of an epigenetic mitotic clock with cancer risk

Supplementary information document with all supplementary figures and their legends. (PDF 1902 kb

Additional file 1: of Correlation of an epigenetic mitotic clock with cancer risk

Blood reference DNA methylation data matrix in Excel format. Detailed legend in file. (XLS 85 kb