Additional file 7 – Supplemental Table 3
Supplemental Table 3a. For HM27 platform (N/%)
Data set 1
total probes
included
CpG island
promoter region
transcribed region
exonic region
intronic region
Filter by SD-b
Data set 2 Data set 4
Data set 6
Breast
Cancer vs
Normal
Colon
Cancer
1000
33.8%
47.0%
53.9%
31.3%
68.7%
1000
74.4%
43.2%
58.4%
33.5%
66.5%
All CpG
Targets
Filtered
Set
Colon
Cancer
Glioblasto
ma
Kidney
Cancer vs
Normal
27578
41.8%
52.2%
49.5%
25.4%
74.6%
22198
46.5%
50.4%
51.3%
26.9%
73.1%
1000
75.4%
39.4%
63.0%
37.5%
62.5%
1000
59.0%
45.3%
56.2%
31.5%
68.5%
1000
21.9%
53.9%
47.0%
27.5%
72.5%
Data set 1
Filter by TM-GOF
Data set 2 Data set 4
Data set 6
Glioblasto
ma
Kidney
Cancer vs
Normal
Breast
Cancer vs
Normal
1000
73.8%
43.4%
58.0%
31.8%
68.2%
1000
79.6%
38.5%
62.4%
37.8%
62.2%
1000
66.9%
42.1%
60.6%
34.2%
65.8%
Supplemental Table 3b. For HM450 platform (N/%)
total probes
included
Type I design
Type II design
CGI Promoter
CGI Exon
CGI Intron
CGI Intergenic
non-CGI Promoter
non-CGI Exon
non-CGI Intron
non-CGI Intergenic
Data set 3
Filter by SD-b
Data set 5
Data set 7
Data set 8
Data set 3
Filter by TM-GOF
Data set 5 Data set 7
Data set 8
All CpG
Targets
Filtered
Set
Glioblasto
ma
Kidney
Cancer vs
Normal
Breast
Cancer vs
Normal
Normal
Blood
Glioblasto
ma
Kidney
Cancer vs
Normal
Breast
Cancer vs
Normal
Normal
Blood
482,421
28.1%
71.9%
384310
29.2%
70.8%
1000
56.3%
43.7%
1000
22.2%
77.8%
1000
36.0%
64.0%
1000
31.0%
69.0%
1000
49.4%
50.6%
1000
27.8%
72.2%
1000
41.8%
58.2%
1000
12.8%
87.2%
21.5%
2.5%
2.9%
4.2%
22.2%
7.0%
20.9%
18.7%
24.8%
3.0%
3.3%
4.8%
21.6%
7.9%
18.9%
15.5%
32.1%
5.4%
6.3%
14.1%
16.2%
3.3%
8.3%
14.3%
5.4%
2.0%
2.2%
2.7%
20.7%
7.3%
33.1%
26.6%
15.6%
2.8%
4.1%
9.0%
20.2%
5.8%
21.4%
21.1%
10.4%
4.3%
5.1%
12.1%
19.4%
3.9%
20.4%
24.4%
55.5%
3.0%
4.8%
9.2%
9.3%
4.3%
9.9%
4.0%
19.1%
4.6%
3.4%
4.5%
15.3%
11.7%
23.7%
17.7%
56.7%
2.9%
2.6%
4.8%
14.6%
5.0%
9.5%
3.9%
16.5%
2.8%
2.4%
5.1%
20.8%
8.1%
27.0%
17.3%