Table 2 Nineteen differentially methylated gene regions in common to early stage tumors.

From: Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes

DMGR

Alternate Gene Name

Basal Med Q

Her2 Med Q

Lum A Med Q

Lum B Med Q

*Any late stage

*All late stage

Present in validation

Validation Median Q

Genomic position of assodciated gene

AGRN Body

AGNR

2.4E-06

1.7E-04

1.8E-07

1.3E-06

Y

—

Y

7.80E-21

chr1:1,020,123–1,056,116

C1orf170 Body

PERM1

4.0E-11

1.7E-05

5.5E-09

9.7E-04

Y

Y

Y

1.31E-08

chr1:975,205–981,029

C1orf170 TSS1500

PERM1

5.4E-04

6.5E-03

7.8E-06

6.8E-05

Y

—

Y

9.23E-03

chr1:975,205–981,029

FAM41C Body

FAM41C

4.1E-03

4.2E-08

1.2E-20

3.4E-03

Y

Y

Y

8.25E-10

chr1:868,071–876,903

FAM41C TSS1500

FAM41C

3.3E-04

1.1E-04

8.4E-05

1.0E-34

Y

Y

Y

1.75E-24

chr1:868,071–876,903

FLJ39609 TSS200

LOC100130417

1.3E-04

6.0E-05

2.9E-06

3.7E-04

Y

Y

Y

5.24E-06

chr1:916,865–921,016

HES4 TSS1500

HES4

3.1E-03

5.2E-04

7.8E-05

2.2E-04

Y

—

Y

5.06E-04

chr1:998,964–1,000,111

ISG15 Body

ISG15

3.1E-07

2.4E-04

1.2E-05

3.6E-04

Y

Y

—

1.03E-01

chr1:1,013,423–1,014,540

KLHL17 3′UTR

KLHL17

3.1E-05

5.5E-07

3.8E-16

2.3E-03

Y

Y

Y

3.99E-08

chr1:960,587–965,715

KLHL17 Body

KLHL17

5.9E-06

1.1E-04

7.9E-04

7.2E-05

Y

—

Y

1.60E-06

chr1:960,587–965,715

NOC2L Body

NOC2L

3.2E-04

6.2E-04

6.6E-05

2.4E-06

Y

Y

Y

4.90E-11

chr1:944,204–959,290

PLEKHN1 3′UTR

PLEKHN1

5.2E-16

4.7E-06

3.1E-07

7.7E-06

Y

—

Y

9.83E-09

chr1:966,497–975,108

PLEKHN1 Body

PLEKHN1

8.9E-10

2.7E-09

7.6E-29

1.7E-30

Y

Y

Y

5.87E-18

chr1:966,497–975,108

PLEKHN1 TSS1500

PLEKHN1

3.1E-05

5.5E-07

2.6E-06

3.6E-07

Y

Y

Y

3.99E-08

chr1:966,497–975,108

PLEKHN1 TSS200

PLEKHN1

1.6E-18

5.8E-10

1.4E-03

1.2E-03

Y

Y

Y

2.93E-10

chr1:966,497–975,108

SAMD11 5′UTR

SAMD11

3.6E-03

7.2E-12

1.0E-09

2.2E-08

Y

Y

Y

4.59E-11

chr1:925,738–944,575

SAMD11 Body

SAMD11

7.1E-08

2.5E-08

8.5E-06

2.0E-04

Y

Y

Y

3.26E-23

chr1:925,738–944,575

SAMD11 TSS1500

SAMD11

2.4E-03

6.1E-04

8.6E-04

1.0E-03

Y

Y

Y

2.02E-05

chr1:925,738–944,575

WASH5P Body

WASH7P

2.9E-03

9.8E-03

1.6E-03

1.3E-05

Y

—

—

7.01E-02

chr1:14,362–29,370

  1. *Reference to any or all breast cancer subtypes in late stage tumors.
Back to article page