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Table 4 DE genes vs qPCR log2 fold changes for all five models reported in this study

From: Inflammation and neuronal gene expression changes differ in early versus late chronic traumatic encephalopathy brain

qPCR\DE

CTE-L

CTE-H

Up

Down

Up

Down

(a) Case vs RHI

 Up

4

11

22

2

 Down

7

11

5

4

 Fisher’s exact

0.57 (0.87)

8.8 (0.034)

 Spearman

− 0.096 (0.59)

0.14 (0.44)

qPCR\DE

CTE-L + RHI

CTE-H

Up

Down

Up

Down

(b) Years of play

 Up

14

9

17

10

 Down

5

5

6

0

 Fisher’s exact

1.5 (0.42)

0 (1.0)

 Spearman

0.27 (0.13)

0.13 (0.47)

qPCR\DE

CTE-L + RHI

CTE-H

Up

Down

Up

Down

(c) AT8

 Up

6

1

16

6

 Down

7

19

6

5

 Fisher’s exact

16.2 (0.0084)

2.2 (0.25)

 Spearman

0.35 (0.047)

0.5 (0.0033)

qPCR\DE

CTE-L + RHI

CTE-H

Up

Down

Up

Down

(d) APOE

 Up

6

8

14

0

 Down

5

14

9

10

 Fisher’s exact

2.1 (0.26)

31 + (0.001)

 Spearman

0.42 (0.014)

0.54 (0.0013)

qPCR\DE

CTE-L + RHI

CTE-H

Up

Down

Up

Down

(e) TMEM106B

 Up

15

5

19

1

 Down

6

7

5

8

 Fisher’s exact

3.5 (0.095)

30.4 (0.0007)

 Spearman

0.34 (0.05)

0.67 (2.38e−5)

  1. Top two rows (qPCR) and columns (mRNASeq) of each table show directional overlap (i.e. positive vs negative log2 fold changes) of 33 genes where both mRNASeq counts and qPCR data are available. Fisher’s Exact rows report odds ratio and associated right-tailed p-value for the contingency tables above. Spearman rows report Spearman correlation and associated p-value for comparing the log2 fold changes between mRNASeq and qPCR.