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Table 4 Putative driver gene sets and metrics in GBM subtypes discovered by QuaDMutNetEx

From: QuaDMutNetEx: a method for detecting cancer driver genes with low mutation frequency

Gene

c

D/R

COSMIC

DDBv2

Gene

c

D/R

COSMIC

DDBv2

Classical GBM

         

Metrics:

 

samples

genes

mutations

Genes in solution

Coverage

Excess coverage

Connected components

 
  

n=69

p=487

1192

6

0.6232

0.1163

5

 

EGFR

21

D

✓

✓

PCDHAC2

15

∙

∙

✓

DNAH9

4

∙

∙

✓

GABRA6

4

∙

∙

✓

PTPRG

2

∙

∙

✓

TEK

2

∙

∙

✓

Mesenchymal GBM

         

Metrics:

 

samples

genes

mutations

Genes in solution

Coverage

Excess coverage

Connected components

 
  

n=75

p=510

1310

12

0.7733

0.1552

4

 

PTEN

23

D

✓

✓

EGFR

17

D

✓

✓

PIK3CA

5

D

✓

✓

CPNE8

3

∙

∙

✓

KDM2B

3

∙

✓

✓

NRXN1

3

∙

∙

✓

INPPL1

3

∙

∙

✓

EZR

2

D

✓

✓

GRB10

2

∙

∙

✓

IRS1

2

D

✓

✓

IRS4

2

∙

∙

✓

LZTR1

2

D

✓

✓

Proneural GBM

         

Metrics:

 

samples

genes

mutations

Genes in solution

Coverage

Excess coverage

Connected components

 
  

n=44

p=229

558

7

0.6364

0.0714

2

 

TP53

15

R

✓

✓

PCDHAC2

5

∙

∙

✓

CHEK1

2

∙

∙

✓

CREBBP

2

D/R

✓

✓

DAXX

2

R

✓

✓

MECOM

2

R

✓

✓

TBP

2

∙

∙

✓

     

Neural GBM

         

Metrics:

 

samples

genes

mutations

Genes in solution

Coverage

Excess coverage

Connected components

 
  

n=41

p=199

482

8

0.6585

0.0370

2

 

TP53

15

R

✓

✓

ANK2

5

∙

∙

✓

PDGFRA

2

D

✓

✓

FLT1

2

∙

∙

✓

PTPN11

2

D

✓

✓

CHD8

2

∙

∙

✓

DYNC1I1

2

∙

∙

✓

KDR

2

D

✓

✓

  1. Boxes below the GBM subtypes show the metrics of a GBM subtype including number of samples, number of genes etc. Discovered genes by QuaDMutNetEx are below the metrics box. Number of patients in the dataset that had a mutation in the gene is in c column. D/R stand for dominant or recessive otherwise unknown. COSMIC [26, 27] column represent if the gene present in COSMIC Cancer Gene Census. Genes present in DriverDBv2 [28] are in DDBv2 column