Classical

List of genes under consideration:
AKT1
AKT3
CDK4
CDKN2A
CDKN2B
EGFR
GAB1
MDM2
MDM4
PIK3C2B
PIK3CA
PIK3CB
SRC

Pairwise

List of alleles with high marginal frequency:
0	AKT1_1
1	AKT3_1
2	CDK4_1
3	CDK4_2
4	CDKN2A_-1
5	CDKN2A_-2
6	CDKN2B_-1
7	CDKN2B_-2
8	EGFR_1
9	EGFR_2
10	GAB1_-1
11	MDM2_1
12	MDM4_1
13	MDM4_2
14	PIK3C2B_1
15	PIK3C2B_2
16	PIK3CA_1
17	PIK3CA_2
18	PIK3CB_1
19	PIK3CB_2
20	SRC_1

List of highly correlated alleles with high frequency of mutation:
1	AKT3_1	12	MDM4_1	1.80156255126e-05
1	AKT3_1	14	PIK3C2B_1	1.80156255126e-05
14	PIK3C2B_1	17	PIK3CA_2	0.0218546386748
14	PIK3C2B_1	19	PIK3CB_2	0.0218546386748
12	MDM4_1	19	PIK3CB_2	0.0218546386748
12	MDM4_1	17	PIK3CA_2	0.0218546386748

List of interaction sets:
1 AKT3_1 12 MDM4_1
1 AKT3_1 14 PIK3C2B_1
12 MDM4_1 19 PIK3CB_2
14 PIK3C2B_1 19 PIK3CB_2
12 MDM4_1 17 PIK3CA_2
14 PIK3C2B_1 17 PIK3CA_2

AKT3_1_MDM4_1
Counts: 72 3 8 8
Path: 0-1-3 Frequency: 0.406169078722 Bootstrap: 3858.0
Path: 0-2-3 Frequency: 0.593830921278 Bootstrap: 6142.0

AKT3_1_PIK3C2B_1
Counts: 72 3 8 8
Path: 0-1-3 Frequency: 0.408575000305 Bootstrap: 3866.0
Path: 0-2-3 Frequency: 0.591424999695 Bootstrap: 6134.0

MDM4_1_PIK3CB_2
Counts: 55 8 15 3 8 6
Path: 0-1-3-5 Frequency: 0.452779344445 Bootstrap: 4980.0
Path: 0-2-3-5 Frequency: 0.210072173916 Bootstrap: 1534.0
Path: 0-2-4-5 Frequency: 0.337148481639 Bootstrap: 3486.0

PIK3C2B_1_PIK3CB_2
Counts: 55 8 15 3 8 6
Path: 0-1-3-5 Frequency: 0.452456534282 Bootstrap: 5002.0
Path: 0-2-3-5 Frequency: 0.21155442545 Bootstrap: 1605.0
Path: 0-2-4-5 Frequency: 0.335989040268 Bootstrap: 3393.0

MDM4_1_PIK3CA_2
Counts: 55 8 15 3 8 6
Path: 0-1-3-5 Frequency: 0.452427957087 Bootstrap: 4986.0
Path: 0-2-3-5 Frequency: 0.210441389214 Bootstrap: 1596.0
Path: 0-2-4-5 Frequency: 0.337130653699 Bootstrap: 3418.0

PIK3C2B_1_PIK3CA_2
Counts: 55 8 15 3 8 6
Path: 0-1-3-5 Frequency: 0.448112555964 Bootstrap: 4909.0
Path: 0-2-3-5 Frequency: 0.213465489073 Bootstrap: 1586.0
Path: 0-2-4-5 Frequency: 0.338421954963 Bootstrap: 3505.0

Three-Way

List of alleles with high marginal frequency:
0	AKT1_1
1	AKT3_1
2	CDK4_1
3	CDK4_2
4	CDKN2A,CDKN2B_-1
5	CDKN2A,CDKN2B_-2
6	EGFR_1
7	EGFR_2
8	GAB1_-1
9	MDM2_1
10	MDM4,PIK3C2B_1
11	MDM4,PIK3C2B_2
12	PIK3CA,PIK3CB_1
13	PIK3CA,PIK3CB_2
14	SRC_1

List of highly correlated alleles with high frequency of mutation:
1	AKT3_1	10	MDM4,PIK3C2B_1	1.80156255126e-05
10	MDM4,PIK3C2B_1	13	PIK3CA,PIK3CB_2	0.0218546386748

List of interaction sets:
1 AKT3_1 10 MDM4,PIK3C2B_1 13 PIK3CA,PIK3CB_2

AKT3_1_MDM4,PIK3C2B_1_PIK3CA,PIK3CB_2
Counts: 51 3 5 4 15 1 2 2 8 1 3 4
Path: 0-1-3-7-11 Frequency: 0.207740583994 Bootstrap: 2903.0
Path: 0-1-5-7-11 Frequency: 0.0655059184429 Bootstrap: 672.0
Path: 0-1-5-9-11 Frequency: 0.0490125483543 Bootstrap: 480.0
Path: 0-2-3-7-11 Frequency: 0.175030006998 Bootstrap: 2120.0
Path: 0-2-6-7-11 Frequency: 0.053346030587 Bootstrap: 275.0
Path: 0-2-6-10-11 Frequency: 0.0407273335322 Bootstrap: 123.0
Path: 0-4-5-7-11 Frequency: 0.0598370142167 Bootstrap: 364.0
Path: 0-4-5-9-11 Frequency: 0.0398381710217 Bootstrap: 148.0
Path: 0-4-6-7-11 Frequency: 0.0608124453002 Bootstrap: 753.0
Path: 0-4-6-10-11 Frequency: 0.0356743280569 Bootstrap: 151.0
Path: 0-4-8-9-11 Frequency: 0.119506342202 Bootstrap: 1301.0
Path: 0-4-8-10-11 Frequency: 0.0929692772941 Bootstrap: 710.0

Pathway

List of genes mapped to networks
AKTSig	PIK3CA	PIK3CB	SRC	GAB1	AKT1	AKT3
RASSig	EGFR
PI3K2Sig	PIK3C2B
P53Sig	CDKN2A	MDM2	MDM4
RBSig	CDKN2A	CDKN2B	CDK4

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

List of highly correlated alleles with high frequency of mutation:

List of pairwise interacting mutations:

List of interaction sets: