Processed files

This page contains the processed files from the original data, including MHBs, ATAC-seq peaks, DNA methylation and gene expression data from TCGA, and single-cell DNA methylation data. When applicable, genomic coordinates were based on hg19.

MHBs

In-house WGBS

Cancer	Assay	Link
BRCA	WGBS	MHB_BRCA.bed.gz
CESC	WGBS	MHB_CESC.bed.gz
COAD	WGBS	MHB_COAD.bed.gz
ESCA	WGBS	MHB_ESCA.bed.gz
HNSC	WGBS	MHB_HNSC.bed.gz
LIHC	WGBS	MHB_LIHC.bed.gz
NSCLC	WGBS	MHB_NSCLC.bed.gz
OV	WGBS	MHB_OV.bed.gz
PACA	WGBS	MHB_PACA.bed.gz
STAD	WGBS	MHB_STAD.bed.gz
THCA	WGBS	MHB_THCA.bed.gz

Cancer MHBs were assigned into 16 clusters and can be downloaded from Cancer MHB cluster.

Public cancer datasets

Cancer	GSE	Assay	Link
CRC	Table S4	RRBS	MHB_CRC.bed.gz
ESCC	GSE149608	WGBS	MHB_ESCC.bed.gz
LIHC	Table S4	WGBS	MHB_LIHC.bed.gz
BRCA	GSE230193	RRBS	CUP_MHB_BRCA.bed.gz
CESC	GSE230193	RRBS	CUP_MHB_CESC.bed.gz
COADREAD	GSE230193	RRBS	CUP_MHB_COADREAD.bed.gz
ESCA	GSE230193	RRBS	CUP_MHB_ESCA.bed.gz
HNSC	GSE230193	RRBS	CUP_MHB_HNSC.bed.gz
LIHC	GSE230193	RRBS	CUP_MHB_LIHC.bed.gz
LUSCLUAD	GSE230193	RRBS	CUP_MHB_LUSCLUAD.bed.gz
OV	GSE230193	RRBS	CUP_MHB_OV.bed.gz
STAD	GSE230193	RRBS	CUP_MHB_STAD.bed.gz
THCA	GSE230193	RRBS	CUP_MHB_THCA.bed.gz

Public normal datasets

Tissue	GSE	Assay	Link
breast	Table S4	WGBS	MHB_breast_normal.bed.gz
colon	Table S4	WGBS	MHB_colon_normal.bed.gz
esophagus	Table S4	WGBS	MHB_esophagus_normal.bed.gz
head_and_neck	Table S4	WGBS	MHB_head_and_neck_normal.bed.gz
liver	Table S4	WGBS	MHB_liver_normal.bed.gz
lung	Table S4	WGBS	MHB_lung_normal.bed.gz
ovary	Table S4	WGBS	MHB_ovary_normal.bed.gz
pancreas	Table S4	WGBS	MHB_pancreas_normal.bed.gz
placenta	Table S4	WGBS	MHB_placenta_normal.bed.gz
stomach	Table S4	WGBS	MHB_stomach_normal.bed.gz
thyroid	Table S4	WGBS	MHB_thyroid_normal.bed.gz

Genomic annotations

Description	Link
FANTOM5 enhancers	FANTOM5_enhancer.bed.gz
TAD in A549	TAD_A549.bed.gz
TAD in HMEC	TAD_HMEC.bed.gz
TAD in IMR90	TAD_IMR90.bed.gz
UCSC promoterss	UCSC_promoters_hg19.bed.gz
Ultraconserved elements	Ultraconserved_elements_hg19.bed.gz
CGI	hg19_cpgIsland.bed.gz
CGI shelves	hg19_cpg_shlves.bed.gz
CGI shores	hg19_cpg_shores.bed.gz
lamin B1 associated domains	laminB1Lads.bed.gz

Genomic segments

Tissue	Status	Link
breast	Normal	breast_N_genomic_segments.bed.gz
breast	Tumor	breast_T_genomic_segments.bed.gz
cervix	Tumor	cervix_T_genomic_segments.bed.gz
colon	Normal	colon_N_genomic_segments.bed.gz
colon	Tumor	colon_T_genomic_segments.bed.gz
esophagus	Normal	esophagus_N_genomic_segments.bed.gz
esophagus	Tumor	esophagus_T_genomic_segments.bed.gz
head and neck	Normal	head_and_neck_N_genomic_segments.bed.gz
head and neck	Tumor	head_and_neck_T_genomic_segments.bed.gz
liver	Normal	liver_N_genomic_segments.bed.gz
liver	Tumor	liver_T_genomic_segments.bed.gz
lung	Normal	lung_N_genomic_segments.bed.gz
lung	Tumor	lung_T_genomic_segments.bed.gz
ovary	Normal	ovary_N_genomic_segments.bed.gz
ovary	Tumor	ovary_T_genomic_segments.bed.gz
pancreas	Normal	pancreas_N_genomic_segments.bed.gz
pancreas	Tumor	pancreas_T_genomic_segments.bed.gz
stomach	Normal	stomach_N_genomic_segments.bed.gz
stomach	Tumor	stomach_T_genomic_segments.bed.gz
thyroid	Normal	thyroid_N_genomic_segments.bed.gz
thyroid	Tumor	thyroid_T_genomic_segments.bed.gz

bedGraph files

Tissue	Status	Link
breast	Normal	breast_N_Merged_Count_CpG.bedGraph.gz
breast	Tumor	breast_T_Merged_Count_CpG.bedGraph.gz
cervix	Tumor	cervix_T_Merged_Count_CpG.bedGraph.gz
colon	Normal	colon_N_Merged_Count_CpG.bedGraph.gz
colon	Tumor	colon_T_Merged_Count_CpG.bedGraph.gz
esophagus	Normal	esophagus_N_Merged_Count_CpG.bedGraph.gz
esophagus	Tumor	esophagus_T_Merged_Count_CpG.bedGraph.gz
head and neck	Normal	head_and_neck_N_Merged_Count_CpG.bedGraph.gz
head and neck	Tumor	head_and_neck_T_Merged_Count_CpG.bedGraph.gz
liver	Normal	liver_N_Merged_Count_CpG.bedGraph.gz
liver	Tumor	liver_T_Merged_Count_CpG.bedGraph.gz
lung	Normal	lung_N_Merged_Count_CpG.bedGraph.gz
lung	Tumor	lung_T_Merged_Count_CpG.bedGraph.gz
ovary	Normal	ovary_N_Merged_Count_CpG.bedGraph.gz
ovary	Tumor	ovary_T_Merged_Count_CpG.bedGraph.gz
pancreas	Normal	pancreas_N_Merged_Count_CpG.bedGraph.gz
pancreas	Tumor	pancreas_T_Merged_Count_CpG.bedGraph.gz
stomach	Normal	stomach_N_Merged_Count_CpG.bedGraph.gz
stomach	Tumor	stomach_T_Merged_Count_CpG.bedGraph.gz
thyroid	Normal	thyroid_N_Merged_Count_CpG.bedGraph.gz
thyroid	Tumor	thyroid_T_Merged_Count_CpG.bedGraph.gz

DMRs (Cancer vs. Normal)

Tissue	Cancer	Link
breast	BRCA	breast_de_novo_DMR.bed.gz
colon	COAD	colon_de_novo_DMR.bed.gz
esophagus	ESCA	esophagus_de_novo_DMR.bed.gz
head	HNSC	head_and_neck_de_novo_DMR.bed.gz
liver	LIHC	liver_de_novo_DMR.bed.gz
lung	NSCLC	lung_de_novo_DMR.bed.gz
ovary	OV	ovary_de_novo_DMR.bed.gz
pancreas	PACA	pancreas_de_novo_DMR.bed.gz
stomach	STAD	stomach_de_novo_DMR.bed.gz
thyroid	THCA	thyroid_de_novo_DMR.bed.gz

TCGA data

	Cancer	ATAC-seq	450K array	Expression (log2TPM)
BRCA	BRCA	BRCA_hg19_peak.bed.gz	BRCA.RData	BRCA.RDS
CESC	CESC	CESC_hg19_peak.bed.gz	CESC.RData	CESC.RDS
COAD	COAD	COAD_hg19_peak.bed.gz	COAD.RData	COAD.RDS
ESCA	ESCA	ESCA_hg19_peak.bed.gz	ESCA.RData	ESCA.RDS
HNSC	HNSC	HNSC_hg19_peak.bed.gz	HNSC.RData	HNSC.RDS
LIHC	LIHC	LIHC_hg19_peak.bed.gz	LIHC.RData	LIHC.RDS
LUAD	LUAD	LUAD_hg19_peak.bed.gz	LUAD.RData	LUAD.RDS
LUSC	LUSC	LUSC_hg19_peak.bed.gz	LUSC.RData	LUSC.RDS
STAD	STAD	STAD_hg19_peak.bed.gz	STAD.RData	STAD.RDS
THCA	THCA	THCA_hg19_peak.bed.gz	THCA.RData	THCA.RDS

ESCC data

The paired ESCC WGBS and RNA-seq data were downloaded from GSE149612.

Description	Link
DMRs	ESCC_T_N_de_novo_DMR.bed.gz
ESCC MHBs	MHB_ESCC.bed.gz
Normal esophagus MHBs	MHB_Esophagus_N.bed.gz
DEGs	ESCC_log2TPM_Wilcox.Rdata
KLF5 ChIP-seq (bigwig)	GSM4274815_TE5_KLF5.SubtractCPM.bw
SOX2 ChIP-seq (bigwig)	GSM5195684_TE10_SOX2.bw

single-cell DNA methylation

Raw data was downloaded from GSE97693.

Description	Link
sc-mHaps	CRC_GSE97693.mhap.gz
MHB: LN	CRC_MHB_LN.bed.gz
MHB:ML	CRC_MHB_ML.bed.gz
MHB:MP	CRC_MHB_MP.bed.gz
MHB:NC	CRC_MHB_NC.bed.gz
MHB:PT	CRC_MHB_PT.bed.gz
MHB:Tumor	CRC_MHB_Tumor.bed.gz
Expression	GSE97693_scRNA_TPM_FPKM.Rdata
Sample annotation	GSE97693_Anno.txt.gz