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Table 1 Genes with novel eQTL in tumors that are also associated with susceptibility

From: Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility

Symbol

Probe

Chr.

Mb

Fold change

SAM q-value

Higher in

Higher genotype

eQTL chr.

eQTL Mb

Gzme

1421227_at

14

56.7

-16.67

<0.01

Resist.

Het.

14

41

Gzme

1450171_x_at

14

56.7

-7.69

<0.01

Resist.

Het.

14

41

Mnda

1452349_x_at

1

175.8

-2.94

4.31

Resist.

Het.

1

169

2310005E10Rik

1453173_at

6

34.3

-2.27

3.02

Resist.

Het.

6

32

Ddx6

1439122_at

9

44.4

-1.82

4.31

Resist.

Hom.

9

34

Spry2

1421656_at

14

106.3

-1.39

3.02

Resist.

Het.

14

94

Kctd3

1436811_at

1

190.8

1.16

4.31

Susc.

Hom.

1

187

Map2k4

1451982_at

11

65.5

1.16

1.38

Susc.

Hom.

11

101

Ssr1

1441327_a_at

13

38.1

1.18

3.02

Susc.

Hom.

10

106

Ndst2

1417931_at

14

21.5

1.21

3.02

Susc.

Hom.

14

19

Ppih

1429832_at

4

119.0

1.23

2.02

Susc.

Hom.

5

44

1810063B07Rik

1427905_at

14

20.9

1.23

1.38

Susc.

Hom.

14

23

Psme3

1418078_at

11

101.2

1.25

3.02

Susc.

Hom.

4

75

Tardbp

1436318_at

4

148.0

1.25

2.02

Susc.

Hom.

1

187

BC003266

1449189_at

4

126.9

1.25

<0.01

Susc.

Hom.

4

121

Acbd6

1452601_a_at

1

157.4

1.26

2.02

Susc.

Het.

9

116

2810457I06Rik

1436805_at

9

40.8

1.26

0.93

Susc.

Het.

9

34

Dhdds

1450654_a_at

4

133.5

1.26

<0.01

Susc.

Hom.

4

141

Nrd1

1424391_at

4

108.7

1.28

0.93

Susc.

Hom.

10

118

Nme6

1448574_at

9

109.7

1.3

0.93

Susc.

Het.

9

102

Sept8

1426802_at

11

53.3

1.35

2.02

Susc.

Hom.

4

106

Hyls1

1431315_at

9

35.4

1.38

1.38

Susc.

Het.

9

34

Pus3

1418491_a_at

9

35.4

1.42

0.93

Susc.

Het.

9

34

C230096C10Rik

1436709_at

4

138.9

1.43

1.38

Susc.

Hom.

4

141

Creg1

1415947_at

1

167.7

1.46

2.02

Susc.

Hom.

1

160

Asah3l

1451355_at

4

86.5

1.51

0.33

Susc.

Hom.

13

1

Rdh11

1449209_a_at

12

80.3

1.57

3.02

Susc.

Het.

6

32

Mtap2

1434194_at

1

66.2

1.81

1.38

Susc.

Hom.

10

102

Tslp

1450004_at

18

33.0

2.34

2.02

Susc.

Het.

5

138

Il18

1417932_at

9

50.4

2.34

<0.01

Susc.

Het.

9

34

  1. Genes that satisfy two conditions: rewired or novel eQTL in tumors compared to normal skin and significant differential expression in papillomas when tumors from resistant and susceptible mice are compared. 'Chr.' and 'Mb' indicate gene location; 'Fold change' indicates differential expression between resistant and susceptible; 'SAM q-value' indicates differential expression significance; 'Higher in' indicates whether the gene was higher in resistant (Resist.) or susceptible (Susc.) animals; 'Higher genotype' indicates whether heterozygous (Het.) or homozygous (Hom.) alleles were associated with higher expression; 'eQTL chr.' and 'eQTL Mb' indicate peak eQTL linkage.
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Genome Biology

ISSN: 1474-760X

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