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Table 1 Summary of genes with significant clusters

From: A spatial simulation approach to account for protein structure when identifying non-random somatic mutations

 

Method

Gene

SpacePAC

iPAC

GraphPAC

NMC

AKT1

<1.00 E-03

4.48 E-04

5.54 E-04

5.55 E-04

ALK

<1.00 E-03

1.99 E-42

3.89 E-35

2.16 E-21

BRAF

<1.00 E-03

<2.23 E-308

<2.23 E-308

<2.23 E-308

CHRM2

1.10 E-02

   

CTNNB1

2.00 E-03

6.69 E-03

1.09 E-03

1.09 E-03

DOCK2

2.20 E-02

9.29 E-03

3.39 E-03

 

FGFR3

2.00 E-02

   

FSHR

2.20 E-02

   

HRAS

<1.00 E-3

1.55 E-23

1.87 E-32

2.68 E-15

IDE

2.00 E-02

3.60 E-03

  

IGF2R

1.40 E-02

 

3.06 E-03

9.04 E-03

KIF18A

6.00 E-03

1.56 E-02

1.56 E-02

1.56 E-02

KRAS

<1.00 E-03

<2.23 E-308

<2.23 E-308

<2.23 E-308

NRAS

<1.00 E-03

1.53 E-75

6.65 E-77

6.77 E-77

PIK3CA

<1.00 E-03

4.73 E-118

4.73 E-118

4.73 E-118

PTEN

<1.00 E-03

5.71 E-03

7.60 E-04

1.68 E-04

SEC23A

1.70 E-02

 

1.18 E-02

 

TP53

<1.00 E-3

1.78 E-134

6.22 E-169

1.08 E-88

  1. This table shows the p-value of the most significant cluster for each of the 18 proteins identified by SpacePAC as well as the corresponding p-value under iPAC, GraphPAC and NMC. A blank entry in position (i,j) signifies that methodology j did not find any structures with significant clustering for protein i. Note that given n i total mutations for protein i, the pairwise methodologies perform n i ( n i 1 ) 2 comparisons, one for each pair of mutations. As such, the p-values shown for iPAC, GraphPAC and NMC have been multiplied by n i ( n i 1 ) 2 in order to account for the multiple comparison and provide a number directly comparable to the SpacePAC p-value. Also, while the GraphPAC methodology was run under all three insertion methods (Cheapest, Nearest and Farthest) as described by [25], we display the minimum p-value over the three methods. Note that since 1000 simulations were used for SpacePAC, the most significant result we can report is p<1.00E−03. Please see Figure 1 for further explanation.