Clinical Features	CN_CNMF		METHLYATION_CNMF		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_CHIERARCHICAL	
	nMutated (%)	nWild-Type	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q
KRAS	11 (6%)	183	0.56523	1	4e-05	0.012	7.9999e-05	0.024	0.00119	0.352	0.00262	0.773	0.00076999	0.229	0.03599	1	0.00019	0.0568
HLA-A	16 (8%)	178	0.25989	1	0.1046	1	0.0085999	1	0.12849	1	0.43433	1	0.0077099	1	0.69561	1	0.41827	1
FBXW7	19 (10%)	175	0.49391	1	0.28957	1	1	1	0.57363	1	0.39957	1	0.4584	1	0.22574	1	0.5414	1
HLA-B	11 (6%)	183	0.51926	1	0.15177	1	0.03353	1	0.099699	1	0.01916	1	0.13465	1	0.01281	1	0.04841	1
PTEN	15 (8%)	179	0.5669	1	0.55716	1	0.050829	1	0.22075	1	0.43291	1	0.1923	1	1	1	0.41812	1
ARID1A	14 (7%)	180	0.0063899	1	0.00334	0.982	0.01207	1	0.00077999	0.232	0.10337	1	0.00445	1	0.70236	1	0.00447	1
MAPK1	9 (5%)	185	0.55169	1	0.25731	1	0.03022	1	0.063399	1	0.18516	1	0.081779	1	0.0211	1	0.02229	1
EP300	21 (11%)	173	1	1	0.15798	1	0.059529	1	0.081109	1	0.84004	1	0.0089299	1	1	1	0.24716	1
PIK3CA	53 (27%)	141	0.03458	1	0.19488	1	0.18977	1	0.03273	1	0.32778	1	0.34426	1	0.48013	1	0.22723	1
NFE2L2	12 (6%)	182	0.92719	1	0.066619	1	0.1339	1	0.066619	1	0.0351	1	0.01825	1	0.38535	1	0.073309	1
FAT2	11 (6%)	183	0.61322	1	0.2996	1	0.085559	1	0.42315	1	0.58295	1	0.76437	1	0.070219	1	0.090729	1
ZNF750	10 (5%)	184	0.085029	1	0.21848	1	0.65262	1	0.1033	1	0.18198	1	0.19055	1	0.47043	1	0.072319	1
BAP1	4 (2%)	190	0.13857	1	0.085189	1	0.085289	1	0.74982	1	0.69035	1	0.35152	1	0.25958	1	0.17227	1
RAB35	4 (2%)	190	0.25953	1	0.14058	1	1	1	0.75094	1	0.47357	1	0.10707	1	0.29566	1	0.03081	1
ERBB3	11 (6%)	183	0.074729	1	0.60376	1	0.0152	1	0.0092299	1	0.079779	1	0.02871	1	0.92856	1	0.3354	1
SMAD4	7 (4%)	187	0.48967	1	0.24956	1	0.4841	1	0.86965	1	0.72475	1	0.59883	1	1	1	0.94574	1
TCTE1	5 (3%)	189	0.18011	1	0.37824	1	0.0155	1	0.39739	1	0.02423	1	0.10086	1	0.20091	1	0.33809	1
NHS	12 (6%)	182	0.86093	1	0.86265	1	0.64342	1	0.2636	1	0.93144	1	0.83442	1	0.42398	1	0.43601	1
LIN9	7 (4%)	187	0.15775	1	0.1644	1	0.89398	1	1	1	0.88646	1	0.27091	1	0.29987	1	0.89201	1
C12ORF43	4 (2%)	190	0.19714	1	0.80171	1	1	1	0.7497	1	0.47328	1	0.20606	1	0.29468	1	0.16146	1
MED1	11 (6%)	183	0.92159	1	0.01948	1	0.03246	1	0.088679	1	0.18797	1	0.24207	1	0.50741	1	0.12417	1
USP28	4 (2%)	190	0.19759	1	0.6653	1	0.45273	1	1	1	0.39239	1	0.93688	1	0.20051	1	0.81945	1
IDS	7 (4%)	187	0.18769	1	0.56619	1	0.79248	1	1	1	0.49487	1	0.21969	1	0.43878	1	0.71516	1
TRIM9	8 (4%)	186	0.33036	1	0.81536	1	0.093789	1	0.56506	1	0.54361	1	0.03779	1	0.56713	1	0.35845	1
SEMA4B	7 (4%)	187	1	1	0.91093	1	0.42745	1	0.12032	1	0.060659	1	0.28835	1	0.39011	1	0.12767	1
ARHGAP4	6 (3%)	188	1	1	0.58857	1	0.32654	1	0.70191	1	0.50938	1	0.22694	1	0.692	1	1	1
POU2F1	3 (2%)	191	0.45252	1	0.38671	1	0.4611	1	0.69819	1	0.63033	1	0.48943	1	0.29271	1	0.16142	1
IFNGR1	6 (3%)	188	1	1	0.39955	1	0.76447	1	1	1	0.32302	1	0.03299	1	0.052859	1	0.78453	1
IGFN1	11 (6%)	183	0.2147	1	0.80719	1	0.72675	1	0.58981	1	0.35587	1	0.96634	1	0.33118	1	0.84877	1
RPGR	9 (5%)	185	1	1	0.87226	1	0.90621	1	0.87634	1	0.91598	1	0.95167	1	0.75857	1	0.80028	1
CASP8	9 (5%)	185	0.67425	1	0.7061	1	0.30757	1	0.45457	1	0.57112	1	0.44933	1	0.12365	1	0.43375	1
GAS6	4 (2%)	190	0.81676	1	0.13721	1	0.35713	1	0.74994	1	1	1	0.39193	1	0.2923	1	0.75485	1
ABCD1	7 (4%)	187	0.60299	1	0.86302	1	0.32443	1	0.13549	1	0.49347	1	0.52001	1	0.056809	1	0.37401	1
RPAP1	4 (2%)	190	0.68155	1	0.72015	1	0.45291	1	1	1	1	1	0.74204	1	1	1	0.90346	1
HIST1H4E	4 (2%)	190	0.19859	1	0.80062	1	0.35723	1	0.30017	1	0.47273	1	0.82835	1	0.4009	1	0.37948	1
NLRC5	7 (4%)	187	0.68007	1	0.099349	1	0.25821	1	0.15567	1	0.13758	1	0.27469	1	0.56508	1	0.1595	1
DDX41	5 (3%)	189	0.02928	1	0.12293	1	0.16991	1	0.39969	1	0.33082	1	0.78386	1	1	1	0.54647	1
MCM7	3 (2%)	191	NA	NA	0.071869	1	NA	NA	NA	NA	1	1	0.4903	1	0.057119	1	0.16279	1