Proneural

List of genes under consideration:
CDK4
CDKN2C
EGFR
MDM2
MDM4
MET
PDGFRA
PIK3C2B
PTEN
TP53

Pairwise

List of alleles with high marginal frequency:
0	CDK4_1
1	CDK4_2
2	CDKN2C_-1
3	CDKN2C_-2
4	EGFR_1
5	EGFR_2
6	MDM2_1
7	MDM2_2
8	MDM4_1
9	MET_1
10	MET_2
11	PDGFRA_1
12	PDGFRA_2
13	PIK3C2B_1
14	PTEN_-1
15	PTEN_-2
16	TP53_-1

List of highly correlated alleles with high frequency of mutation:
4	EGFR_1	9	MET_1	3.17804354346e-15
9	MET_1	14	PTEN_-1	1.51604653348e-06
1	CDK4_2	7	MDM2_2	2.2608997679e-06
4	EGFR_1	14	PTEN_-1	5.5874496687e-06
5	EGFR_2	9	MET_1	2.92729076484e-05
5	EGFR_2	14	PTEN_-1	0.000263256514385
4	EGFR_1	15	PTEN_-2	0.00464180334019
12	PDGFRA_2	16	TP53_-1	0.0110696038604
9	MET_1	15	PTEN_-2	0.0171971834509
13	PIK3C2B_1	16	TP53_-1	0.0187200470728
8	MDM4_1	16	TP53_-1	0.0187200470728
1	CDK4_2	14	PTEN_-1	0.0191728527541
8	MDM4_1	12	PDGFRA_2	0.0425900427614
12	PDGFRA_2	13	PIK3C2B_1	0.0425900427614

List of interaction sets:
1 CDK4_2 7 MDM2_2
1 CDK4_2 14 PTEN_-1
4 EGFR_1 15 PTEN_-2
5 EGFR_2 9 MET_1
5 EGFR_2 14 PTEN_-1
8 MDM4_1 16 TP53_-1
8 MDM4_1 12 PDGFRA_2
9 MET_1 15 PTEN_-2
12 PDGFRA_2 16 TP53_-1
12 PDGFRA_2 13 PIK3C2B_1
13 PIK3C2B_1 16 TP53_-1

CDK4_2_MDM2_2
Counts: 87 1 20 1 5 1 2 1 11
Path: 0-1-2-5-8 Frequency: 0.330988889878 Bootstrap: 4708.0
Path: 0-1-4-5-8 Frequency: 0.0832836352892 Bootstrap: 322.0
Path: 0-1-4-7-8 Frequency: 0.162009614755 Bootstrap: 1009.0
Path: 0-3-4-5-8 Frequency: 0.0606544676813 Bootstrap: 133.0
Path: 0-3-4-7-8 Frequency: 0.104423306917 Bootstrap: 266.0
Path: 0-3-6-7-8 Frequency: 0.258640085479 Bootstrap: 3562.0

CDK4_2_PTEN_-1
Counts: 30 4 5 50 2 25
Path: 0-1-2-5 Frequency: 0.311406982607 Bootstrap: 2400.0
Path: 0-1-4-5 Frequency: 0.0918883410224 Bootstrap: 0.0
Path: 0-3-4-5 Frequency: 0.596704676371 Bootstrap: 7600.0

EGFR_1_PTEN_-2
Counts: 27 9 17 43 3 8
Path: 0-1-3-5 Frequency: 0.437161494496 Bootstrap: 6264.0
Path: 0-2-3-5 Frequency: 0.379493636384 Bootstrap: 3431.0
Path: 0-2-4-5 Frequency: 0.18334486912 Bootstrap: 305.0

EGFR_2_MET_1
Counts: 36 5 6 7 50 14
Path: 0-1-2-5 Frequency: 0.283210688869 Bootstrap: 2518.0
Path: 0-1-4-5 Frequency: 0.243193952616 Bootstrap: 1122.0
Path: 0-3-4-5 Frequency: 0.473595358515 Bootstrap: 6360.0

EGFR_2_PTEN_-1
Counts: 27 9 3 17 43 17
Path: 0-1-2-5 Frequency: 0.264230829345 Bootstrap: 1171.0
Path: 0-1-4-5 Frequency: 0.265069174056 Bootstrap: 997.0
Path: 0-3-4-5 Frequency: 0.4706999966 Bootstrap: 7832.0

MDM4_1_TP53_-1
Counts: 79 14 17 10
Path: 0-1-3 Frequency: 0.465936432277 Bootstrap: 4430.0
Path: 0-2-3 Frequency: 0.534063567723 Bootstrap: 5570.0

MDM4_1_PDGFRA_2
Counts: 68 13 10 2 19 10
Path: 0-1-3-5 Frequency: 0.396974285837 Bootstrap: 4696.0
Path: 0-2-3-5 Frequency: 0.181089299644 Bootstrap: 102.0
Path: 0-2-4-5 Frequency: 0.421936414519 Bootstrap: 5202.0

MET_1_PTEN_-2
Counts: 26 10 17 53 4 8
Path: 0-1-3-5 Frequency: 0.461629417318 Bootstrap: 7511.0
Path: 0-2-3-5 Frequency: 0.374836331339 Bootstrap: 2398.0
Path: 0-2-4-5 Frequency: 0.163534251343 Bootstrap: 91.0

PDGFRA_2_TP53_-1
Counts: 70 9 19 13 3 12
Path: 0-1-2-5 Frequency: 0.429055519911 Bootstrap: 5192.0
Path: 0-1-4-5 Frequency: 0.171709410491 Bootstrap: 51.0
Path: 0-3-4-5 Frequency: 0.399235069598 Bootstrap: 4757.0

PDGFRA_2_PIK3C2B_1
Counts: 68 10 19 13 2 10
Path: 0-1-2-5 Frequency: 0.427578109189 Bootstrap: 5374.0
Path: 0-1-4-5 Frequency: 0.189020769644 Bootstrap: 86.0
Path: 0-3-4-5 Frequency: 0.383401121167 Bootstrap: 4540.0

PIK3C2B_1_TP53_-1
Counts: 79 14 17 10
Path: 0-1-3 Frequency: 0.465981682299 Bootstrap: 4392.0
Path: 0-2-3 Frequency: 0.534018317701 Bootstrap: 5608.0

Three-Way

List of alleles with high marginal frequency:
0	CDK4_1
1	CDK4_2
2	CDKN2C_-1
3	CDKN2C_-2
4	EGFR_1
5	EGFR_2
6	MDM2_1
7	MDM2_2
8	MDM4,PIK3C2B_1
9	MET_1
10	MET_2
11	PDGFRA_1
12	PDGFRA_2
13	PTEN_-1
14	PTEN_-2
15	TP53_-1

List of highly correlated alleles with high frequency of mutation:
4	EGFR_1	9	MET_1	3.17804354346e-15
9	MET_1	13	PTEN_-1	1.51604653348e-06
1	CDK4_2	7	MDM2_2	2.2608997679e-06
4	EGFR_1	13	PTEN_-1	5.5874496687e-06
5	EGFR_2	9	MET_1	2.92729076484e-05
5	EGFR_2	13	PTEN_-1	0.000263256514385
4	EGFR_1	14	PTEN_-2	0.00464180334019
12	PDGFRA_2	15	TP53_-1	0.0110696038604
9	MET_1	14	PTEN_-2	0.0171971834509
8	MDM4,PIK3C2B_1	15	TP53_-1	0.0187200470728
1	CDK4_2	13	PTEN_-1	0.0191728527541
8	MDM4,PIK3C2B_1	12	PDGFRA_2	0.0425900427614

List of interaction sets:
1 CDK4_2 5 EGFR_2 13 PTEN_-1
1 CDK4_2 7 MDM2_2 13 PTEN_-1
4 EGFR_1 9 MET_1 14 PTEN_-2
5 EGFR_2 9 MET_1 13 PTEN_-1
5 EGFR_2 9 MET_1 14 PTEN_-2
8 MDM4,PIK3C2B_1 12 PDGFRA_2 15 TP53_-1

CDK4_2_EGFR_2_PTEN_-1
Counts: 21 4 4 8 1 2 3 1 1 13 1 5 28 2 15 11 1 7
Path: 0-1-2-5-8-17 Frequency: 0.0116467001864 Bootstrap: 7.0
Path: 0-1-2-5-14-17 Frequency: 0.0464523226463 Bootstrap: 249.0
Path: 0-1-2-11-14-17 Frequency: 0.0722364333226 Bootstrap: 468.0
Path: 0-1-4-5-8-17 Frequency: 0.00629640253801 Bootstrap: 0.0
Path: 0-1-4-5-14-17 Frequency: 0.0271138451482 Bootstrap: 70.0
Path: 0-1-4-7-8-17 Frequency: 0.0253608710986 Bootstrap: 44.0
Path: 0-1-4-7-16-17 Frequency: 0.0133275233507 Bootstrap: 6.0
Path: 0-1-4-13-14-17 Frequency: 0.00865040611096 Bootstrap: 4.0
Path: 0-1-4-13-16-17 Frequency: 0.00101933828928 Bootstrap: 0.0
Path: 0-1-10-11-14-17 Frequency: 0.0451441060837 Bootstrap: 30.0
Path: 0-1-10-13-14-17 Frequency: 0.0117288037435 Bootstrap: 2.0
Path: 0-1-10-13-16-17 Frequency: 0.00162705637891 Bootstrap: 0.0
Path: 0-3-4-5-8-17 Frequency: 0.00706481311343 Bootstrap: 4.0
Path: 0-3-4-5-14-17 Frequency: 0.0323686502368 Bootstrap: 250.0
Path: 0-3-4-7-8-17 Frequency: 0.0279118637912 Bootstrap: 186.0
Path: 0-3-4-7-16-17 Frequency: 0.0147968485673 Bootstrap: 85.0
Path: 0-3-4-13-14-17 Frequency: 0.00753909894406 Bootstrap: 21.0
Path: 0-3-4-13-16-17 Frequency: 0.000866848553884 Bootstrap: 0.0
Path: 0-3-6-7-8-17 Frequency: 0.108968282546 Bootstrap: 2090.0
Path: 0-3-6-7-16-17 Frequency: 0.0521347053843 Bootstrap: 804.0
Path: 0-3-6-15-16-17 Frequency: 0.0536314205567 Bootstrap: 585.0
Path: 0-3-12-13-14-17 Frequency: 0.029435832158 Bootstrap: 28.0
Path: 0-3-12-13-16-17 Frequency: 0.00299257712183 Bootstrap: 0.0
Path: 0-3-12-15-16-17 Frequency: 0.0434354549689 Bootstrap: 78.0
Path: 0-9-10-11-14-17 Frequency: 0.104020788627 Bootstrap: 1796.0
Path: 0-9-10-13-14-17 Frequency: 0.0191500974111 Bootstrap: 101.0
Path: 0-9-10-13-16-17 Frequency: 0.0026025288774 Bootstrap: 0.0
Path: 0-9-12-13-14-17 Frequency: 0.0875164006447 Bootstrap: 932.0
Path: 0-9-12-13-16-17 Frequency: 0.00935334210492 Bootstrap: 1.0
Path: 0-9-12-15-16-17 Frequency: 0.125606637495 Bootstrap: 2159.0

CDK4_2_MDM2_2_PTEN_-1
Counts: 30 1 4 1 4 1 1 1 2 50 1 17 1 2 1 1 1 9
Path: 0-1-2-5-8-17 Frequency: 0.0546764377248 Bootstrap: 634.0
Path: 0-1-2-5-14-17 Frequency: 0.0117098806364 Bootstrap: 101.0
Path: 0-1-2-11-14-17 Frequency: 0.101704199732 Bootstrap: 1258.0
Path: 0-1-4-5-8-17 Frequency: 0.0199937854469 Bootstrap: 64.0
Path: 0-1-4-5-14-17 Frequency: 0.00723552245898 Bootstrap: 24.0
Path: 0-1-4-7-8-17 Frequency: 0.0194328326771 Bootstrap: 51.0
Path: 0-1-4-7-16-17 Frequency: 0.0129532712611 Bootstrap: 52.0
Path: 0-1-4-13-14-17 Frequency: 0.00687952884307 Bootstrap: 12.0
Path: 0-1-4-13-16-17 Frequency: 0.0123203191584 Bootstrap: 39.0
Path: 0-1-10-11-14-17 Frequency: 0.0182624059268 Bootstrap: 2.0
Path: 0-1-10-13-14-17 Frequency: 0.0026346659722 Bootstrap: 0.0
Path: 0-1-10-13-16-17 Frequency: 0.0067956204506 Bootstrap: 2.0
Path: 0-3-4-5-8-17 Frequency: 0.0235253598834 Bootstrap: 131.0
Path: 0-3-4-5-14-17 Frequency: 0.00921947118137 Bootstrap: 60.0
Path: 0-3-4-7-8-17 Frequency: 0.0266710327038 Bootstrap: 143.0
Path: 0-3-4-7-16-17 Frequency: 0.0177487749725 Bootstrap: 141.0
Path: 0-3-4-13-14-17 Frequency: 0.0101251163641 Bootstrap: 43.0
Path: 0-3-4-13-16-17 Frequency: 0.0156427296113 Bootstrap: 58.0
Path: 0-3-6-7-8-17 Frequency: 0.0488293856215 Bootstrap: 503.0
Path: 0-3-6-7-16-17 Frequency: 0.0259997745059 Bootstrap: 205.0
Path: 0-3-6-15-16-17 Frequency: 0.07650726782 Bootstrap: 766.0
Path: 0-3-12-13-14-17 Frequency: 0.00685774938829 Bootstrap: 4.0
Path: 0-3-12-13-16-17 Frequency: 0.00872780029582 Bootstrap: 5.0
Path: 0-3-12-15-16-17 Frequency: 0.0243571679537 Bootstrap: 28.0
Path: 0-9-10-11-14-17 Frequency: 0.126973302627 Bootstrap: 1923.0
Path: 0-9-10-13-14-17 Frequency: 0.0192211630389 Bootstrap: 80.0
Path: 0-9-10-13-16-17 Frequency: 0.0521420920761 Bootstrap: 504.0
Path: 0-9-12-13-14-17 Frequency: 0.0406509632389 Bootstrap: 407.0
Path: 0-9-12-13-16-17 Frequency: 0.0549668457372 Bootstrap: 534.0
Path: 0-9-12-15-16-17 Frequency: 0.137235532692 Bootstrap: 2226.0

EGFR_1_MET_1_PTEN_-2
Counts: 22 3 5 6 13 2 3 39 3 2 1 7
Path: 0-1-3-7-11 Frequency: 0.207937389 Bootstrap: 3265.0
Path: 0-1-5-7-11 Frequency: 0.091896978929 Bootstrap: 1473.0
Path: 0-1-5-9-11 Frequency: 0.0328178733575 Bootstrap: 34.0
Path: 0-2-3-7-11 Frequency: 0.177701769181 Bootstrap: 1768.0
Path: 0-2-6-7-11 Frequency: 0.069693549115 Bootstrap: 276.0
Path: 0-2-6-10-11 Frequency: 0.0203788026894 Bootstrap: 0.0
Path: 0-4-5-7-11 Frequency: 0.0911459454364 Bootstrap: 668.0
Path: 0-4-5-9-11 Frequency: 0.0334110183274 Bootstrap: 50.0
Path: 0-4-6-7-11 Frequency: 0.060531061304 Bootstrap: 442.0
Path: 0-4-6-10-11 Frequency: 0.0164318166497 Bootstrap: 9.0
Path: 0-4-8-9-11 Frequency: 0.145264566612 Bootstrap: 1617.0
Path: 0-4-8-10-11 Frequency: 0.0527892293983 Bootstrap: 398.0

EGFR_2_MET_1_PTEN_-1
Counts: 22 3 3 5 6 1 13 2 4 3 39 13
Path: 0-1-2-5-11 Frequency: 0.0606858212943 Bootstrap: 687.0
Path: 0-1-2-8-11 Frequency: 0.139045061066 Bootstrap: 1886.0
Path: 0-1-4-5-11 Frequency: 0.0117868335351 Bootstrap: 5.0
Path: 0-1-4-10-11 Frequency: 0.0708729262683 Bootstrap: 228.0
Path: 0-1-7-8-11 Frequency: 0.0190244921219 Bootstrap: 2.0
Path: 0-1-7-10-11 Frequency: 0.0296476940006 Bootstrap: 45.0
Path: 0-3-4-5-11 Frequency: 0.0322758326524 Bootstrap: 90.0
Path: 0-3-4-10-11 Frequency: 0.188763222672 Bootstrap: 2673.0
Path: 0-3-9-10-11 Frequency: 0.0842894883192 Bootstrap: 373.0
Path: 0-6-7-8-11 Frequency: 0.0935957081282 Bootstrap: 790.0
Path: 0-6-7-10-11 Frequency: 0.122170191377 Bootstrap: 1287.0
Path: 0-6-9-10-11 Frequency: 0.147842728565 Bootstrap: 1934.0

EGFR_2_MET_1_PTEN_-2
Counts: 22 3 3 5 6 1 13 2 4 3 39 13 3 2 1 1 7 2
Path: 0-1-2-5-11-17 Frequency: 0.0477125117335 Bootstrap: 906.0
Path: 0-1-2-8-11-17 Frequency: 0.130764380884 Bootstrap: 3209.0
Path: 0-1-2-8-14-17 Frequency: 0.0365198657787 Bootstrap: 474.0
Path: 0-1-4-5-11-17 Frequency: 0.0135398536793 Bootstrap: 9.0
Path: 0-1-4-10-11-17 Frequency: 0.0243322379459 Bootstrap: 17.0
Path: 0-1-4-10-16-17 Frequency: 0.0326527591656 Bootstrap: 45.0
Path: 0-1-7-8-11-17 Frequency: 0.0169730345943 Bootstrap: 16.0
Path: 0-1-7-8-14-17 Frequency: 0.00516387078142 Bootstrap: 8.0
Path: 0-1-7-10-11-17 Frequency: 0.0099844758016 Bootstrap: 7.0
Path: 0-1-7-10-16-17 Frequency: 0.0134116798788 Bootstrap: 7.0
Path: 0-1-7-13-14-17 Frequency: 0.00240084575991 Bootstrap: 0.0
Path: 0-1-7-13-16-17 Frequency: 0.00762260112291 Bootstrap: 5.0
Path: 0-3-4-5-11-17 Frequency: 0.0378342568788 Bootstrap: 273.0
Path: 0-3-4-10-11-17 Frequency: 0.0652047213667 Bootstrap: 578.0
Path: 0-3-4-10-16-17 Frequency: 0.0876763432046 Bootstrap: 1580.0
Path: 0-3-9-10-11-17 Frequency: 0.0318177784385 Bootstrap: 90.0
Path: 0-3-9-10-16-17 Frequency: 0.0419379407354 Bootstrap: 307.0
Path: 0-3-9-15-16-17 Frequency: 0.0285680189345 Bootstrap: 68.0
Path: 0-6-7-8-11-17 Frequency: 0.0386167647639 Bootstrap: 97.0
Path: 0-6-7-8-14-17 Frequency: 0.011117690932 Bootstrap: 31.0
Path: 0-6-7-10-11-17 Frequency: 0.021703343246 Bootstrap: 30.0
Path: 0-6-7-10-16-17 Frequency: 0.0289115046688 Bootstrap: 87.0
Path: 0-6-7-13-14-17 Frequency: 0.00484541498415 Bootstrap: 8.0
Path: 0-6-7-13-16-17 Frequency: 0.0160157884356 Bootstrap: 25.0
Path: 0-6-9-10-11-17 Frequency: 0.0278163825179 Bootstrap: 49.0
Path: 0-6-9-10-16-17 Frequency: 0.037283094666 Bootstrap: 154.0
Path: 0-6-9-15-16-17 Frequency: 0.0243095849416 Bootstrap: 48.0
Path: 0-6-12-13-14-17 Frequency: 0.0200318275565 Bootstrap: 175.0
Path: 0-6-12-13-16-17 Frequency: 0.0663577049991 Bootstrap: 774.0
Path: 0-6-12-15-16-17 Frequency: 0.0688737216038 Bootstrap: 923.0

MDM4,PIK3C2B_1_PDGFRA_2_TP53_-1
Counts: 60 9 8 2 13 5 9 5 3 1 7 6
Path: 0-1-3-5-11 Frequency: 0.106845768876 Bootstrap: 1024.0
Path: 0-1-3-9-11 Frequency: 0.0346017713086 Bootstrap: 83.0
Path: 0-1-7-9-11 Frequency: 0.177355594343 Bootstrap: 1753.0
Path: 0-2-3-5-11 Frequency: 0.0691040683942 Bootstrap: 433.0
Path: 0-2-3-9-11 Frequency: 0.0276122801339 Bootstrap: 137.0
Path: 0-2-4-5-11 Frequency: 0.0482641321393 Bootstrap: 19.0
Path: 0-2-4-10-11 Frequency: 0.0895019549463 Bootstrap: 137.0
Path: 0-2-8-9-11 Frequency: 0.0164152224779 Bootstrap: 1.0
Path: 0-2-8-10-11 Frequency: 0.0367122594649 Bootstrap: 9.0
Path: 0-6-7-9-11 Frequency: 0.281771112189 Bootstrap: 5561.0
Path: 0-6-8-9-11 Frequency: 0.0289971012698 Bootstrap: 58.0
Path: 0-6-8-10-11 Frequency: 0.0828187344574 Bootstrap: 785.0

Pathway

List of genes mapped to networks
AKTSig	PTEN
RASSig	PDGFRA	EGFR	MET
PI3K2Sig	PIK3C2B
P53Sig	TP53	MDM2	MDM4
RBSig	CDKN2C	CDK4

List of alleles with high marginal frequency:
0	AKTSig_1
1	RASSig_1
2	PI3K2Sig_1
3	P53Sig_-1
4	RBSig_-1

List of highly correlated alleles with high frequency of mutation:
2	PI3K2Sig_1	3	P53Sig_-1	6.38150972562e-12
0	AKTSig_1	1	RASSig_1	0.000106725136715
1	RASSig_1	3	P53Sig_-1	0.00457961890856
3	P53Sig_-1	4	RBSig_-1	0.0320939248353

List of interaction sets:
0 AKTSig_1 1 RASSig_1
1 RASSig_1 3 P53Sig_-1
2 PI3K2Sig_1 3 P53Sig_-1
3 P53Sig_-1 4 RBSig_-1

AKTSig_1_RASSig_1
Counts: 18 12 20 74
Path: 0-1-3 Frequency: 0.398099890927 Bootstrap: 1151.0
Path: 0-2-3 Frequency: 0.601900109073 Bootstrap: 8849.0

RASSig_1_P53Sig_-1
Counts: 23 46 7 48
Path: 0-1-3 Frequency: 0.749852197015 Bootstrap: 9987.0
Path: 0-2-3 Frequency: 0.250147802985 Bootstrap: 13.0

PI3K2Sig_1_P53Sig_-1
Counts: 68 1 28 27
Path: 0-1-3 Frequency: 0.234922086877 Bootstrap: 1270.0
Path: 0-2-3 Frequency: 0.765077913123 Bootstrap: 8730.0

P53Sig_-1_RBSig_-1
Counts: 45 26 24 29
Path: 0-1-3 Frequency: 0.480185332327 Bootstrap: 3509.0
Path: 0-2-3 Frequency: 0.519814667673 Bootstrap: 6491.0