Cohort	BCR	Clinical	CN	LowP	Methylation	mRNA	mRNASeq	miR	miRSeq	RPPA	MAF	rawMAF
ACC-TP	92	92	90	0	80	0	79	0	80	46	90	0
ACC-NB	87	87	85	0	0	0	0	0	0	0	0	0
ACC-NT	5	5	5	0	0	0	0	0	0	0	0	0
ACC	92	92	90	0	80	0	79	0	80	46	90	0
BLCA-TP	412	412	410	112	412	0	408	0	409	344	130	395
BLCA-TM	1	1	1	0	1	0	0	0	1	0	0	1
BLCA-NB	390	390	361	98	0	0	0	0	0	0	0	0
BLCA-NT	36	36	34	22	21	0	19	0	19	0	0	0
BLCA-FFPE	0	0	2	0	3	0	0	0	3	0	0	0
BLCA	412	412	410	112	412	0	408	0	409	344	130	395
BRCA-TP	1098	1097	1089	19	1097	526	1093	0	1078	887	977	0
BRCA-TM	7	7	7	0	7	3	7	0	7	5	5	0
BRCA-NB	1009	1008	979	19	0	0	0	0	0	0	0	0
BRCA-NT	162	162	134	0	124	61	112	0	104	45	0	0
BRCA-FFPE	0	0	7	0	7	0	0	0	12	0	0	0
BRCA	1098	1097	1089	19	1097	526	1093	0	1078	887	977	0
CESC-TM	2	2	2	0	2	0	2	0	2	0	0	0
CESC-TP	307	307	295	50	307	0	304	0	307	173	194	0
CESC-NB	298	298	281	48	0	0	0	0	0	0	0	0
CESC-NT	8	8	8	2	3	0	3	0	3	0	0	0
CESC	307	307	295	50	307	0	304	0	307	173	194	0
CHOL-TP	51	45	36	0	36	0	36	0	36	30	35	0
CHOL-NT	15	15	15	0	9	0	9	0	9	0	0	0
CHOL-NB	34	34	34	0	0	0	0	0	0	0	0	0
CHOL	51	45	36	0	36	0	36	0	36	30	35	0
COAD-TR	1	1	1	0	1	0	1	0	1	0	0	0
COAD-TP	460	458	451	69	457	153	457	0	406	360	154	367
COAD-TM	2	2	1	0	1	0	1	0	0	2	0	0
COAD-NB	419	417	375	55	0	0	0	0	0	0	0	0
COAD-NT	93	93	90	14	75	19	41	0	0	0	0	0
COAD-FFPE	0	0	12	0	12	0	0	0	3	0	0	0
COAD	460	458	451	69	457	153	457	0	406	360	154	367
COADREAD-TR	2	2	2	0	2	0	2	0	2	1	0	0
COADREAD-TP	631	629	616	104	622	222	623	0	549	491	223	489
COADREAD-TM	2	2	1	0	1	0	1	0	0	2	0	0
COADREAD-NB	575	573	508	86	0	0	0	0	0	0	0	0
COADREAD-NT	110	110	107	18	87	22	51	0	0	0	0	0
COADREAD-FFPE	0	0	12	0	12	0	0	0	3	0	0	0
COADREAD	631	629	616	104	622	222	623	0	549	491	223	489
DLBC-TP	58	48	48	0	48	0	48	0	47	33	48	0
DLBC-NB	46	44	44	0	0	0	0	0	0	0	0	0
DLBC-NBM	4	4	4	0	0	0	0	0	0	0	0	0
DLBC	58	48	48	0	48	0	48	0	47	33	48	0
ESCA-TM	1	1	1	0	1	0	1	0	1	0	0	0
ESCA-TP	185	185	184	51	185	0	184	0	184	126	185	0
ESCA-NB	126	126	124	35	0	0	0	0	0	0	0	0
ESCA-NT	65	65	64	18	16	0	13	0	13	0	0	0
ESCA	185	185	184	51	185	0	184	0	184	126	185	0
FPPP-TR	1	1	0	0	0	0	0	0	0	0	0	0
FPPP-TP	38	38	0	0	0	0	0	0	23	0	0	0
FPPP-NB	37	37	0	0	0	0	0	0	0	0	0	0
FPPP-NT	24	24	0	0	0	0	0	0	0	0	0	0
FPPP-FFPE	0	0	0	0	0	0	0	0	22	0	0	0
FPPP	38	38	0	0	0	0	0	0	23	0	0	0
GBM-TR	13	13	13	0	13	0	13	0	0	11	7	7
GBM-TP	613	595	577	0	420	540	153	565	0	233	283	283
GBM-NB	505	501	488	0	0	0	0	0	0	0	0	0
GBM-NT	49	38	26	0	2	10	5	10	5	0	0	0
GBM	613	595	577	0	420	540	160	565	0	238	290	290
GBMLGG-TR	27	27	27	0	27	0	27	0	14	17	7	21
GBMLGG-TP	1129	1110	1090	52	936	567	669	565	512	662	569	799
GBMLGG-NB	1016	1011	974	52	0	0	0	0	0	0	0	0
GBMLGG-NBC	2	2	2	0	0	0	0	0	0	0	0	0
GBMLGG-NT	51	40	26	0	2	10	5	10	5	0	0	0
GBMLGG	1129	1110	1090	52	936	567	676	565	512	668	576	806
HNSC-TM	2	2	2	0	2	0	2	0	2	0	0	2
HNSC-TP	528	528	522	108	528	0	520	0	523	357	279	510
HNSC-NT	82	82	74	18	50	0	44	0	44	0	0	0
HNSC-NB	508	508	492	99	0	0	0	0	0	0	0	0
HNSC	528	528	522	108	528	0	520	0	523	357	279	510
KICH-TP	113	113	66	0	66	0	66	0	66	63	66	66
KICH-NB	9	9	9	0	0	0	0	0	0	0	0	0
KICH-NT	57	57	57	0	0	0	25	0	25	0	0	0
KICH	113	113	66	0	66	0	66	0	66	63	66	66
KIPAN-TAP	2	2	1	0	2	0	2	0	2	1	0	0
KIPAN-TP	973	941	883	0	892	88	889	0	873	756	644	799
KIPAN-NB	364	354	338	0	0	0	0	0	0	0	0	0
KIPAN-NT	607	585	562	0	409	0	129	0	130	0	0	0
KIPAN-FFPE	0	0	3	0	3	0	0	0	4	0	0	0
KIPAN	973	941	883	0	892	88	889	0	873	756	644	799
KIRC-TAP	1	1	1	0	1	0	1	0	1	0	0	0
KIRC-TP	537	537	528	0	535	72	533	0	516	478	417	451
KIRC-NB	115	115	110	0	0	0	0	0	0	0	0	0
KIRC-NT	440	440	420	0	359	0	72	0	71	0	0	0
KIRC-FFPE	0	0	3	0	3	0	0	0	4	0	0	0
KIRC	537	537	528	0	535	72	533	0	516	478	417	451
KIRP-TAP	1	1	0	0	1	0	1	0	1	1	0	0
KIRP-TP	323	291	289	0	291	16	290	0	291	215	161	282
KIRP-NB	240	230	219	0	0	0	0	0	0	0	0	0
KIRP-NT	110	88	85	0	50	0	32	0	34	0	0	0
KIRP	323	291	289	0	291	16	290	0	291	215	161	282
LAML-TB	200	200	197	0	194	0	179	0	188	0	197	0
LAML-NT	200	200	195	0	0	0	0	0	0	0	0	0
LAML	200	200	197	0	194	0	179	0	188	0	197	0
LGG-TR	14	14	14	0	14	0	14	0	14	6	0	14
LGG-TP	516	515	513	52	516	27	516	0	512	429	286	516
LGG-NB	511	510	486	52	0	0	0	0	0	0	0	0
LGG-NBC	2	2	2	0	0	0	0	0	0	0	0	0
LGG-NT	2	2	0	0	0	0	0	0	0	0	0	0
LGG	516	515	513	52	516	27	516	0	512	430	286	516
LIHC-TR	2	2	2	0	2	0	2	0	2	0	0	0
LIHC-TP	377	377	370	0	377	0	371	0	372	184	198	373
LIHC-NB	327	327	305	0	0	0	0	0	0	0	0	0
LIHC-NT	89	89	83	0	50	0	50	0	50	0	0	0
LIHC	377	377	370	0	377	0	371	0	372	184	198	373
LUAD-TR	2	2	2	0	2	0	2	0	2	0	0	1
LUAD-TP	585	522	516	120	578	32	515	0	513	365	230	542
LUAD-NB	417	417	401	73	0	0	0	0	0	0	0	0
LUAD-NT	184	184	176	56	56	0	59	0	46	0	0	0
LUAD-FFPE	0	0	12	0	11	0	0	0	3	0	0	0
LUAD	585	522	516	120	578	32	515	0	513	365	230	542
LUSC-TP	504	504	501	0	503	154	501	0	478	328	178	0
LUSC-NB	317	317	296	0	0	0	0	0	0	0	0	0
LUSC-NT	249	249	238	0	69	0	51	0	45	0	0	0
LUSC	504	504	501	0	503	154	501	0	478	328	178	0
MESO-TP	87	87	87	0	87	0	87	0	87	63	0	0
MESO-NT	1	1	1	0	0	0	0	0	0	0	0	0
MESO-NB	86	86	85	0	0	0	0	0	0	0	0	0
MESO	87	87	87	0	87	0	87	0	87	63	0	0
OV-TR	12	12	18	0	18	17	4	18	8	11	0	2
OV-TP	601	590	583	0	592	572	303	568	453	425	316	467
OV-NB	454	453	441	0	0	0	0	0	0	0	0	0
OV-NT	133	125	130	0	12	8	0	8	0	0	0	0
OV	602	591	586	0	594	574	304	570	453	426	316	469
PAAD-TM	1	1	1	0	1	0	1	0	1	0	0	1
PAAD-TP	185	185	184	0	184	0	178	0	178	123	150	184
PAAD-NB	153	153	146	0	0	0	0	0	0	0	0	0
PAAD-NT	37	37	37	0	10	0	4	0	4	0	0	0
PAAD	185	185	184	0	184	0	178	0	178	123	150	184
PANGI-TR	2	2	2	0	2	0	2	0	2	1	0	0
PANGI-TP	1259	1257	1242	262	1250	222	1222	0	1169	974	697	884
PANGI-TM	3	3	2	0	2	0	2	0	1	2	0	0
PANGI-NB	1096	1094	1001	192	0	0	0	0	0	0	0	0
PANGI-NT	276	276	266	72	130	22	97	0	54	0	0	0
PANGI-FFPE	0	0	12	0	12	0	0	0	3	0	0	0
PANGI	1259	1257	1242	262	1250	222	1222	0	1169	974	697	884
PCPG-TAP	3	3	3	0	3	0	3	0	3	1	3	0
PCPG-TP	179	179	175	0	179	0	179	0	179	79	179	0
PCPG-TM	2	2	2	0	2	0	2	0	2	2	2	0
PCPG-NB	177	177	175	0	0	0	0	0	0	0	0	0
PCPG-NT	5	5	5	0	3	0	3	0	3	0	0	0
PCPG	179	179	175	0	179	0	179	0	179	80	179	0
PRAD-TP	499	499	492	115	498	0	497	0	494	352	332	498
PRAD-TM	1	1	1	0	1	0	1	0	1	0	0	1
PRAD-NB	439	439	423	103	0	0	0	0	0	0	0	0
PRAD-NT	117	117	113	12	50	0	52	0	52	0	0	0
PRAD-FFPE	1	1	6	0	4	0	0	0	4	0	0	0
PRAD	499	499	492	115	498	0	497	0	494	352	332	498
READ-TR	1	1	1	0	1	0	1	0	1	1	0	0
READ-TP	171	171	165	35	165	69	166	0	143	131	69	122
READ-NB	156	156	133	31	0	0	0	0	0	0	0	0
READ-NT	17	17	17	4	12	3	10	0	0	0	0	0
READ	171	171	165	35	165	69	166	0	143	131	69	122
SARC-TR	3	3	3	0	3	0	3	0	3	3	0	0
SARC-TP	261	261	257	0	261	0	259	0	259	223	247	0
SARC-TM	1	1	1	0	1	0	1	0	1	0	0	0
SARC-NB	240	240	233	0	0	0	0	0	0	0	0	0
SARC-NT	23	23	22	0	4	0	2	0	0	0	0	0
SARC	261	261	257	0	261	0	259	0	259	223	247	0
SKCM-TP	109	109	104	18	105	0	103	0	97	92	67	81
SKCM-TM	368	368	367	102	367	0	368	0	352	262	278	287
SKCM-TAM	2	2	0	0	1	0	1	0	1	1	0	0
SKCM-NB	469	469	465	118	0	0	0	0	0	0	0	0
SKCM-NT	3	3	2	0	2	0	1	0	2	0	0	0
SKCM	470	470	469	118	470	0	469	0	448	353	343	366
STAD-TP	443	443	442	107	443	0	415	0	436	357	289	395
STAD-NT	101	101	95	36	27	0	35	0	41	0	0	0
STAD-NB	395	395	369	71	0	0	0	0	0	0	0	0
STAD	443	443	442	107	443	0	415	0	436	357	289	395
STES-TM	1	1	1	0	1	0	1	0	1	0	0	0
STES-TP	628	628	626	158	628	0	599	0	620	483	474	395
STES-NB	521	521	493	106	0	0	0	0	0	0	0	0
STES-NT	166	166	159	54	43	0	46	0	54	0	0	0
STES	628	628	626	158	628	0	599	0	620	483	474	395
TGCT-TAP	6	5	6	0	6	0	6	0	6	4	6	0
TGCT-TP	150	134	150	0	150	0	150	0	150	118	149	0
TGCT-NB	150	134	148	0	0	0	0	0	0	0	0	0
TGCT	150	134	150	0	150	0	150	0	150	118	149	0
THCA-TM	8	8	7	1	8	0	8	0	8	2	4	8
THCA-TP	503	503	499	97	503	0	501	0	502	368	401	496
THCA-NB	429	429	411	92	0	0	0	0	0	0	0	0
THCA-NT	100	100	96	13	56	0	59	0	59	0	0	0
THCA	503	503	499	98	503	0	501	0	502	368	402	496
THYM-TP	124	124	123	0	124	0	120	0	124	90	123	0
THYM-NBC	2	2	2	0	0	0	0	0	0	0	0	0
THYM-NB	111	111	111	0	0	0	0	0	0	0	0	0
THYM-NT	13	13	12	0	2	0	2	0	2	0	0	0
THYM	124	124	123	0	124	0	120	0	124	90	123	0
UCEC-TR	1	1	1	0	1	0	1	0	1	0	0	0
UCEC-TP	560	548	540	106	547	54	545	0	538	440	248	0
UCEC-NB	524	524	504	104	0	0	0	0	0	0	0	0
UCEC-NT	51	39	49	3	47	0	35	0	33	0	0	0
UCEC-FFPE	0	0	4	0	4	0	0	0	3	0	0	0
UCEC	560	548	540	106	547	54	545	0	538	440	248	0
UCS-TP	57	57	56	0	57	0	57	0	56	48	57	0
UCS-NT	6	6	6	0	0	0	0	0	0	0	0	0
UCS-NB	51	51	49	0	0	0	0	0	0	0	0	0
UCS	57	57	56	0	57	0	57	0	56	48	57	0
UVM-TP	80	80	80	51	80	0	80	0	80	12	80	0
UVM-NB	80	80	80	51	0	0	0	0	0	0	0	0
UVM	80	80	80	51	80	0	80	0	80	12	80	0
Totals	11368	11196	10987	1211	10972	2217	10267	1135	10156	7841	7099	6322