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Table 8 Methylation, expression analysis of pooled dataset focusing only on thyroid-cancer associated genes.

From: A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology

 

Pooled Dataset

 

DMR(FDR)

DE (FDR)

FDRs Combined

Methylation Change (percentage)

RAP1GAP

1.29E-05

4.42E-10

1.93E-13

-32.37%

TIMP3

-

1.46E-03

-

-31.69%

DAPK

2.14E-04

1.26E-11

3.35E-12

24.69%

SLC5A8

-

4.80E-04

1.99E-04

-11.61%

RARB

7.43E-03

6.77E-07

1.01E-07

-17.92%

TSHR

6.58E-06

1.05E-07

8.96E-06

-18.12%

RASSF6

-

1.05E-07

2.31E-08

3.85%

CDKN2A

-

1.57E-11

4.87E-11

2.92%

MLH1

-

-

-

-1.10%

FN1

7.00E-04

3.78E-16

1.16E-17

-39.43%

FOXE1

-

-

-

1.00%

HGF

-

7.65E-03

-

-1.54%

KRT19

2.36E-03

2.83E-18

3.17E-19

-9.87%

LGALS3

9.21E-05

1.46E-19

7.22E-22

-9.98%

MET

1.09E-04

1.99E-26

1.50E-28

-45.69%

RET

3.08E-03

1.01E-04

4.96E-06

-15.86%

KISS1R

1.08E-03

5.98E-11

2.02E-12

-4.12%

ADAMTS5

7.80E-05

-

8.94E-03

28.55%

HOXB4

1.07E-03

-

7.07E-03

-3.21%

TCL1B

5.29E-03

-

1.55E-06

-35.67%

NOTCH4

6.85E-03

4.37E-04

4.10E-05

-13.05%

RASSF1

1.62E-03

-

5.08E-03

19.06%

PPARG

-

1.41E-05

7.76E-06

-2.22%

ALK

4.69E-04

3.79E-13

6.63E-15

9.44%

NTRK3

-

4.74E-03

4.15E-03

-1.44%

  1. Pooled dataset results showing Differential Methylation (DMR), Differential Expression (DE), Combination of Differential Methylation and Differential Expression Significances (FDRs Combined) and Methylation Change in %. Only the values with Differential Expression and Differential Methylation Significances below 0.01 are shown on the table. FDR>0.01 are shown as blank. Moreover, methylation change >15% are shown as bold. Combining methylation and expression values greatly improves detecting thyroid-associated-genes as significantly altered.
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