Supplemental Files for publication "The causes and consequences of human-specific DNA methylation"

Supplemental Files for publication "The causes and consequences of human-specific DNA methylation" S1_regulation_CpG_sites (Referred to in the main text and supplemental figures as Supplemental File 1): csv files containing per-CpG site regulatory classification of DA, CNCC, IPSC, HEP, SKM using beta-binomial framework. Each row corresponds to a single CpG site, with columns indicating its genomic position, allele-specific methylation differences in parental and hybrid samples, statistical significance of cis and trans effects, and the resulting regulatory category (pure_cis, pure_trans, cis_plus_trans, cis_x_trans, or conserved). S2_regulation_promoters (Referred to in the main text and supplemental figures as Supplemental File 2): csv files containing per-promoter regulatory classification of DA, CNCC, IPSC, HEP, SKM. Each row corresponds to a promoter region, with columns indicating its genomic position, allele-specific methylation differences in parental and hybrid samples, statistical significance of cis and trans effects, and the resulting regulatory category (pure_cis, pure_trans, cis_plus_trans, cis_x_trans, or conserved). S3_regulation_DMRs (Referred to in the main text and supplemental figures as Supplemental File 3): csv file containing de novo DMRs identified using changepoint detection and results from S1. Each row corresponds to a DMR, with columns indicating its genomic position, allele-specific methylation differences in parental and hybrid samples, statistical significance of cis and trans effects, and the resulting regulatory category (pure_cis, pure_trans, cis_plus_trans, cis_x_trans, or conserved). S4_transDMR_motifs (Referred to in the main text and supplemental figures as Supplemental File 4): Motif analysis results using de novo trans-DMRs identified from S3. Fold enrichment, p-values and Benjamini-Hochberg corrected q-values are reported in Hu>Ch and Hu<Ch trans-DMRs in DA, CNCC, IPSC, HEP, SKM. S5_gene_expression (Referred to in the main text and supplemental figures as Supplemental File 5): TMM normalized gene expression for between-cell type comparisons are reported in TMM_normalized. Hybrid and Parental log2(Human/Chimpanzee) gene expression and corresponding p-values and adjusted p-values are reported in TPM_log2FC. S6_expression_methylation_correlation (Referred to in the main text and supplemental figures as Supplemental File 6): Methylation–expression correlation of "cis-cis" genes, "trans-trans" genes and all genes from DA and CNCC are reported in genomic bins 1kb upstream and downstream of TSS. Correlation coefficients, significance as well as number of CpG sites per bin are reported. S7_SignTest (Referred to in the main text and supplemental figures as Supplemental File 7): All HPO and KEGG pathways and related enrichment statistics from binomial sign test are reported. File "methylation" shows results from methylation-only, and file "repressive_methylation_only" shows results from integrating expression and methylation data and applying the sign test on genes with repressive methylation.