Table 1 Mutual exclusivity analysis of PNKP and candidate mutations that were found in the patient’s tumor sample.

From: Mutations of the DNA repair gene PNKP in a patient with microcephaly, seizures, and developmental delay (MCSZ) presenting with a high-grade brain tumor

A

B

Neither

A not B

B not A

Both

Log2 Odds ratio

p value

q value

Tendency

PNKP

BRCA2

9520

97

546

28

2.331

< 0.001

< 0.001

Co-occurrence

PNKP

ATRX

9394

101

672

24

1.732

< 0.001

< 0.001

Co-occurrence

PNKP

NF1

9274

102

792

23

1.401

< 0.001

< 0.001

Co-occurrence

PNKP

RB1

9320

103

746

22

1.416

< 0.001

< 0.001

Co-occurrence

PNKP

TP53

6258

63

3808

62

0.694

0.005

0.007

Co-occurrence

PNKP

CDK4

9787

120

279

5

0.548

0.269

0.283

Co-occurrence

  1. Mutual exclusivity between PNKP and candidate mutations in TCGA PanCancer Atlas studies in cBioPortal. Neither: Numbers of samples with alterations in neither A or B. Only A/Only B: Numbers of samples with alterations in only gene A/B. Both A + B: Numbers of samples with alterations in both gene A and B. Log2 odds ratio: Quantifies how strongly the presence or absence of alterations in A are associated with the presence or absence of alterations in B in the selected samples. OR = (Neither * Both)/(A Not B * B Not A). Log2 odds ratio > 0: Tendency towards co-occurrence. Log2 odds ratio < = 0: Tendency towards mutual exclusivity. p-value: derived from one-side Fisher Exact Test. q-Value: derived from Benjamini–Hochberg FDR correction procedure.
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