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A
B
ZONE 1
ZONE 2
ZONE 3
ZONE 1
FANK1
GSDMDC1
PPIL6
SUHW4
SLC43A1
ZONE 2
AMDHD1
DNER
FBXO15
HCFC2
LEPREL1
NANOS1
TGFBI
ZONE3
BAIAP3
BARHL1
BCL2L12
CAT
CD274
EXOC2
RNF185
MSH3
SEC63
ZIM2
U
U
U
U
U
+
+
+
+
+
+
+
+
+
+
U
U
U
U
U
U
M
+
+
+
+
+
+
-
+
+
+
+
+
+
+
U
U
U
U
U
U
U
U
U
M
+
+
+
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
+
+
2/22(9%)
Methylation in HCT116
Expression in HCT116
Expression in DKO
Sensitivity of detecting hypermethylated genes compared with control genes.
Methylation in HCT116
Expression in HCT116
Expression in DKO
Figure S1.
C
ZONE 1
AMFR
FLNB
U + +
U + +
ZONE2
ZONE3
ABCA3
ABCB10
ACADM
ADAMTS15
ADAMTS18
CHL1
CIC
CNNM4
DBN1
EYA4
KEAP1
NF1
SYNE2
U
U
U
M
M
M
U
U
U
M
U
U
U
+ +
+ +
+ +
- +
- - + +
+ +
ND
- +
ND
+ +
ND
4/15(27%)
Figure S1. Sensitivity of detecting hypermethylated genes compared with control genes. (A) Scatter plot of gene
expression changes in HCT116 cells treated with either DAC (Y-axis) or TSA (X-axis). Gene names are abbreviated
using ENSMBL nomenclature; orange shaded names indicate randomly selected genes outside the top and next tier
TSA negative zone while blue indicates such randomly selected CAN genes in these zones (all CAN genes selected
and which had CpG islands grouped in zone 3 as defined below). The blue or orange spots indicate the location of
control genes in TSA responsive zones (green box= Zone 1 and contains genes with a negative TSA response or
charcoal box = Zone 2 containing genes with expression increases with either both TSA and DAC or TSA alone), and
the DAC unresponsive zone within the TSA negative response zone (pink box = Zone 3). (B) Rates for validation of
methylation and expression of randomly selected control genes outside the top and next tier zones within the negative
TSA responsive zone. Gene names are shaded to indicate the zone in which they were located (green, charcoal or
pink). Methylation status is shown as U, unmethylated, or M, methylated and expression was assessed as either
positive (+) or negative (-). The cell line in which the analysis was performed (either HCT116 or DKO) is indicated at
the top of the column. Numbers of validated genes are indicated at the bottom with percentage of positive genes
shown in parentheses (C) Validation of methylation and expression of randomly selected CAN genes which fell outside
the top and next tier zones within the TSA negative response zone. Gene names are shaded to indicate the zone in
which they were located (green or pink). Methylation status is shown as U, unmethylated, or M, methylated and
expression was assessed as either positive (+) or negative (-). The cell line in which the analysis was performed (either
HCT116 or DKO) is indicated at the top of the column. Numbers of validated genes are indicated at the bottom with
percentage of positive genes shown in parentheses.