Table 1 Sources of methylation and expression data.

Tissue Type	Reference	Data Source	Type
Breast Tumor	[23]	GEO (GSE31979)	Methylation (Inf 27k)
Colorectal Tumor	[5]	GEO (GSE25062)	Methylation (Inf 27k)
Prostate Tumor	[24]	GEO (GSE26126)	Methylation (Inf 27k)
Glioblastoma	[8]	TCGA [22]	Methylation (Inf 27k)
Lung Tumors	[22]	TCGA [22]	Methylation (Inf 27k)
AML	[22]	TCGA [22]	Methylation (Inf 27k)
Ovarian Tumors	[25]	TCGA [22]	Methylation (Inf 27k)
Normal Tissues	[18]	GEO (GSE26990)	Methylation (Inf 27k)
Normal Tissues	[81]	GEO (GSE30090)	Methylation (Inf 27k)
Colorectal Tumors	[38]	Publication Supplementary Dataset S1 [40]	Methylation (MBD-seq)
Colorectal Tumors	[39]	SRA (SRA029584)	Methylation (MBD-seq)
Colorectal Tumor	[37]	Author's Website [41]	Methylation (WG bis-seq)
Breast Tumors	[7]	GEO (GSE26349)	Methylation (Inf 27k)
Breast Tumors	[18]	GEO (GSE26990)	Methylation (Inf 27k)
Breast Tumors	[28]	Author's Website [82]	Methylation (Inf 27k)
Normal Tissues	[36]	GEO (GSE2361)	Expression (Affy 133A)
Normal Tissues	[34]	SRA (SRA008403)	Expression (RNA-seq)
Normal Breast Tissue Cell Fractions	[85]	GEO (GSE16997)	Expression (Ill v3)
Normal Colon and Liver	[89]	GEO (GSE13471)	Expression (Affy 133plus2)

Details of data sources used in each study. The tissue type found in each dataset, the study this data were taken from, the data type and the source of the original data used are indicated. GEO and SRA accession numbers are included in the table along with links to data from other sources. Inf 27k, Illumina Infinium HumanMethylation27 BeadChip array; MBD-seq, Methyl Binding Domain pull-down followed by sequencing; WG bis-seq, whole genome bisulfite sequencing; Affy 133A, Affymetrix U133A genechip; Affy 133plus2, Affymetrix U133plus2 genechip; Ill v3,Illumina WG6 V3.0 human beadchips. Data from Noushmehr et al. 2011 (Glioblastoma methylation)[8] and TCGA 2011 (Ovarian tumor methylation)[25] were limited to IDs identified in these publications when downloaded from the TCGA website[22]. Methylation data from lung tumors and AML were downloaded from the TCGA website on 19 October 2011. AML, acute myeloid leukemia.

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