Correlation between copy number variation genes (focal events) and molecular subtypes

Skin Cutaneous Melanoma (Metastatic)

15 January 2014 | analyses__2014_01_15

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C17D2SN5

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 40 focal events and 10 molecular subtypes across 292 patients, 25 significant findings detected with P value < 0.05 and Q value < 0.25.

1q cnv correlated to 'CN_CNMF'.
6p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
6q cnv correlated to 'CN_CNMF'.
7p cnv correlated to 'CN_CNMF'.
7q cnv correlated to 'CN_CNMF'.
8q cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
9p cnv correlated to 'CN_CNMF'.
10p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
10q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
11q cnv correlated to 'CN_CNMF'.
12p cnv correlated to 'CN_CNMF'.
13q cnv correlated to 'CN_CNMF'.
14q cnv correlated to 'CN_CNMF'.
19p cnv correlated to 'CN_CNMF'.
19q cnv correlated to 'CN_CNMF'.
20p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
20q cnv correlated to 'CN_CNMF'.
xq cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 40 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 25 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
10q	182 (62%)	110	1.9e-09 (7.59e-07)	0.0509 (1.00)	0.794 (1.00)	0.0893 (1.00)	4.4e-06 (0.00172)	2.13e-05 (0.00826)	0.737 (1.00)	0.0503 (1.00)	0.561 (1.00)	0.484 (1.00)
6p	173 (59%)	119	6.65e-07 (0.000264)	5.69e-05 (0.0219)	0.793 (1.00)	0.0729 (1.00)	0.13 (1.00)	0.0166 (1.00)	0.351 (1.00)	0.1 (1.00)	0.399 (1.00)	0.193 (1.00)
8q	155 (53%)	137	4.15e-06 (0.00163)	0.00511 (1.00)	0.292 (1.00)	0.909 (1.00)	0.000357 (0.135)	0.0447 (1.00)	0.345 (1.00)	0.305 (1.00)	0.227 (1.00)	0.566 (1.00)
10p	173 (59%)	119	1.35e-08 (5.37e-06)	0.0396 (1.00)	0.905 (1.00)	0.208 (1.00)	2.82e-05 (0.0109)	0.000678 (0.254)	0.696 (1.00)	0.00546 (1.00)	0.686 (1.00)	0.133 (1.00)
20p	140 (48%)	152	1.74e-05 (0.00677)	0.014 (1.00)	0.778 (1.00)	0.826 (1.00)	0.00051 (0.192)	0.0247 (1.00)	0.316 (1.00)	0.0273 (1.00)	0.157 (1.00)	0.392 (1.00)
xq	103 (35%)	189	0.00259 (0.953)	1.43e-07 (5.69e-05)	0.101 (1.00)	0.165 (1.00)	7.17e-05 (0.0275)	0.00258 (0.95)	0.142 (1.00)	0.392 (1.00)	0.326 (1.00)	0.561 (1.00)
1q	150 (51%)	142	1.89e-06 (0.000746)	0.061 (1.00)	0.16 (1.00)	0.631 (1.00)	0.00537 (1.00)	0.153 (1.00)	0.474 (1.00)	0.247 (1.00)	0.181 (1.00)	0.123 (1.00)
6q	183 (63%)	109	0.000322 (0.123)	0.204 (1.00)	0.93 (1.00)	0.213 (1.00)	0.0201 (1.00)	0.112 (1.00)	0.637 (1.00)	0.155 (1.00)	0.88 (1.00)	0.0849 (1.00)
7p	171 (59%)	121	2.96e-06 (0.00116)	0.666 (1.00)	0.0882 (1.00)	0.718 (1.00)	0.019 (1.00)	0.188 (1.00)	0.354 (1.00)	0.26 (1.00)	0.525 (1.00)	0.535 (1.00)
7q	169 (58%)	123	1.02e-06 (0.000404)	0.887 (1.00)	0.326 (1.00)	0.874 (1.00)	0.0307 (1.00)	0.28 (1.00)	0.807 (1.00)	0.202 (1.00)	0.79 (1.00)	0.51 (1.00)
9p	208 (71%)	84	8.3e-07 (0.000329)	0.0064 (1.00)	0.269 (1.00)	0.473 (1.00)	0.00271 (0.996)	0.0178 (1.00)	0.587 (1.00)	0.122 (1.00)	0.882 (1.00)	0.509 (1.00)
11q	141 (48%)	151	0.000113 (0.0434)	0.209 (1.00)	0.804 (1.00)	0.526 (1.00)	0.0325 (1.00)	0.197 (1.00)	0.504 (1.00)	0.21 (1.00)	0.773 (1.00)	0.892 (1.00)
12p	93 (32%)	199	0.000449 (0.17)	0.04 (1.00)	0.898 (1.00)	0.768 (1.00)	0.0104 (1.00)	0.0256 (1.00)	0.978 (1.00)	0.568 (1.00)	0.393 (1.00)	0.746 (1.00)
13q	136 (47%)	156	0.000234 (0.0893)	0.12 (1.00)	0.0903 (1.00)	0.965 (1.00)	0.0389 (1.00)	0.372 (1.00)	0.496 (1.00)	0.236 (1.00)	0.771 (1.00)	0.119 (1.00)
14q	123 (42%)	169	3.26e-05 (0.0126)	0.302 (1.00)	0.864 (1.00)	0.682 (1.00)	0.00804 (1.00)	0.107 (1.00)	0.441 (1.00)	0.367 (1.00)	0.559 (1.00)	0.8 (1.00)
19p	103 (35%)	189	0.000357 (0.135)	0.0154 (1.00)	0.633 (1.00)	0.233 (1.00)	0.0156 (1.00)	0.224 (1.00)	0.382 (1.00)	0.989 (1.00)	0.241 (1.00)	0.774 (1.00)
19q	102 (35%)	190	0.00053 (0.199)	0.00572 (1.00)	0.513 (1.00)	0.102 (1.00)	0.00751 (1.00)	0.0164 (1.00)	0.297 (1.00)	0.965 (1.00)	0.358 (1.00)	0.774 (1.00)
20q	152 (52%)	140	1.52e-05 (0.00594)	0.0274 (1.00)	0.831 (1.00)	0.764 (1.00)	0.0111 (1.00)	0.225 (1.00)	0.762 (1.00)	0.0267 (1.00)	0.243 (1.00)	0.56 (1.00)
1p	102 (35%)	190	0.0411 (1.00)	0.153 (1.00)	0.756 (1.00)	0.823 (1.00)	0.00332 (1.00)	0.0275 (1.00)	0.273 (1.00)	0.16 (1.00)	0.207 (1.00)	0.831 (1.00)
2p	94 (32%)	198	0.0301 (1.00)	0.185 (1.00)	0.21 (1.00)	0.18 (1.00)	0.331 (1.00)	0.189 (1.00)	0.861 (1.00)	0.401 (1.00)	0.566 (1.00)	0.375 (1.00)
2q	92 (32%)	200	0.0555 (1.00)	0.16 (1.00)	0.271 (1.00)	0.497 (1.00)	0.17 (1.00)	0.0785 (1.00)	0.736 (1.00)	0.348 (1.00)	0.392 (1.00)	0.213 (1.00)
3p	93 (32%)	199	0.713 (1.00)	0.672 (1.00)	0.67 (1.00)	0.195 (1.00)	0.0664 (1.00)	0.0737 (1.00)	0.271 (1.00)	0.0243 (1.00)	0.0283 (1.00)	0.472 (1.00)
3q	92 (32%)	200	0.391 (1.00)	0.825 (1.00)	0.379 (1.00)	0.124 (1.00)	0.0359 (1.00)	0.114 (1.00)	0.448 (1.00)	0.00797 (1.00)	0.0932 (1.00)	0.752 (1.00)
4p	106 (36%)	186	0.0649 (1.00)	0.265 (1.00)	0.691 (1.00)	0.27 (1.00)	0.255 (1.00)	0.0689 (1.00)	0.828 (1.00)	0.757 (1.00)	0.893 (1.00)	0.9 (1.00)
4q	101 (35%)	191	0.162 (1.00)	0.63 (1.00)	0.306 (1.00)	0.258 (1.00)	0.0705 (1.00)	0.0678 (1.00)	0.192 (1.00)	0.382 (1.00)	0.349 (1.00)	0.482 (1.00)
5p	123 (42%)	169	0.011 (1.00)	0.227 (1.00)	0.96 (1.00)	0.56 (1.00)	0.846 (1.00)	0.913 (1.00)	0.132 (1.00)	0.267 (1.00)	0.229 (1.00)	0.364 (1.00)
5q	118 (40%)	174	0.102 (1.00)	0.194 (1.00)	0.196 (1.00)	0.166 (1.00)	0.856 (1.00)	0.757 (1.00)	0.15 (1.00)	0.318 (1.00)	0.0558 (1.00)	0.376 (1.00)
8p	146 (50%)	146	0.00113 (0.422)	0.195 (1.00)	0.397 (1.00)	0.828 (1.00)	0.00475 (1.00)	0.142 (1.00)	0.549 (1.00)	0.221 (1.00)	0.483 (1.00)	0.649 (1.00)
9q	170 (58%)	122	0.113 (1.00)	0.0692 (1.00)	0.222 (1.00)	0.0156 (1.00)	0.0329 (1.00)	0.284 (1.00)	0.466 (1.00)	0.447 (1.00)	0.803 (1.00)	0.346 (1.00)
11p	131 (45%)	161	0.0028 (1.00)	0.124 (1.00)	0.835 (1.00)	0.728 (1.00)	0.00171 (0.635)	0.0267 (1.00)	0.809 (1.00)	0.212 (1.00)	0.719 (1.00)	0.991 (1.00)
12q	81 (28%)	211	0.0153 (1.00)	0.15 (1.00)	0.974 (1.00)	0.689 (1.00)	0.0979 (1.00)	0.149 (1.00)	0.981 (1.00)	0.863 (1.00)	0.811 (1.00)	0.976 (1.00)
15q	107 (37%)	185	0.0181 (1.00)	0.329 (1.00)	0.234 (1.00)	0.738 (1.00)	0.0213 (1.00)	0.0324 (1.00)	0.231 (1.00)	0.00229 (0.846)	0.253 (1.00)	0.162 (1.00)
16p	98 (34%)	194	0.00513 (1.00)	0.00184 (0.682)	0.103 (1.00)	0.552 (1.00)	0.0525 (1.00)	0.206 (1.00)	0.979 (1.00)	0.299 (1.00)	0.931 (1.00)	0.983 (1.00)
16q	120 (41%)	172	0.0143 (1.00)	0.0436 (1.00)	0.0809 (1.00)	0.72 (1.00)	0.287 (1.00)	0.486 (1.00)	0.837 (1.00)	0.405 (1.00)	0.794 (1.00)	0.822 (1.00)
17p	131 (45%)	161	0.417 (1.00)	0.723 (1.00)	0.673 (1.00)	0.741 (1.00)	0.478 (1.00)	0.897 (1.00)	0.809 (1.00)	0.973 (1.00)	0.852 (1.00)	0.924 (1.00)
17q	105 (36%)	187	0.298 (1.00)	0.399 (1.00)	0.217 (1.00)	0.17 (1.00)	0.525 (1.00)	0.66 (1.00)	0.808 (1.00)	0.842 (1.00)	0.285 (1.00)	0.182 (1.00)
18p	131 (45%)	161	0.0371 (1.00)	0.437 (1.00)	0.926 (1.00)	0.634 (1.00)	0.125 (1.00)	0.281 (1.00)	0.77 (1.00)	0.595 (1.00)	0.212 (1.00)	0.935 (1.00)
18q	117 (40%)	175	0.105 (1.00)	0.624 (1.00)	0.988 (1.00)	0.588 (1.00)	0.474 (1.00)	0.521 (1.00)	0.824 (1.00)	0.441 (1.00)	0.65 (1.00)	0.896 (1.00)
21q	108 (37%)	184	0.231 (1.00)	0.107 (1.00)	0.323 (1.00)	0.963 (1.00)	0.144 (1.00)	0.205 (1.00)	0.459 (1.00)	0.574 (1.00)	0.208 (1.00)	0.555 (1.00)
22q	136 (47%)	156	0.00161 (0.6)	0.103 (1.00)	0.929 (1.00)	0.971 (1.00)	0.316 (1.00)	0.387 (1.00)	0.716 (1.00)	0.397 (1.00)	0.676 (1.00)	0.855 (1.00)

'1q' versus 'CN_CNMF'

P value = 1.89e-06 (Fisher's exact test), Q value = 0.00075

Table S1. Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
1Q MUTATED	76	39	35
1Q WILD-TYPE	34	41	67

Figure S1. Get High-res Image Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'CN_CNMF'

P value = 6.65e-07 (Fisher's exact test), Q value = 0.00026

Table S2. Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
6P MUTATED	86	42	45
6P WILD-TYPE	24	38	57

Figure S2. Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 5.69e-05 (Fisher's exact test), Q value = 0.022

Table S3. Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	108	112
6P MUTATED	56	66	51
6P WILD-TYPE	16	42	61

Figure S3. Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'CN_CNMF'

P value = 0.000322 (Fisher's exact test), Q value = 0.12

Table S4. Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
6Q MUTATED	79	56	48
6Q WILD-TYPE	31	24	54

Figure S4. Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 2.96e-06 (Fisher's exact test), Q value = 0.0012

Table S5. Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
7P MUTATED	65	63	43
7P WILD-TYPE	45	17	59

Figure S5. Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'CN_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 4e-04

Table S6. Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
7Q MUTATED	62	64	43
7Q WILD-TYPE	48	16	59

Figure S6. Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'CN_CNMF'

P value = 4.15e-06 (Fisher's exact test), Q value = 0.0016

Table S7. Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
8Q MUTATED	69	52	34
8Q WILD-TYPE	41	28	68

Figure S7. Get High-res Image Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'MRNASEQ_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.14

Table S8. Gene #16: '8q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	79	110
8Q MUTATED	64	30	57
8Q WILD-TYPE	30	49	53

Figure S8. Get High-res Image Gene #16: '8q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p' versus 'CN_CNMF'

P value = 8.3e-07 (Fisher's exact test), Q value = 0.00033

Table S9. Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
9P MUTATED	82	71	55
9P WILD-TYPE	28	9	47

Figure S9. Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 1.35e-08 (Fisher's exact test), Q value = 5.4e-06

Table S10. Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
10P MUTATED	67	66	40
10P WILD-TYPE	43	14	62

Figure S10. Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.011

Table S11. Gene #19: '10p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	79	110
10P MUTATED	73	37	58
10P WILD-TYPE	21	42	52

Figure S11. Get High-res Image Gene #19: '10p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q' versus 'CN_CNMF'

P value = 1.9e-09 (Fisher's exact test), Q value = 7.6e-07

Table S12. Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
10Q MUTATED	68	70	44
10Q WILD-TYPE	42	10	58

Figure S12. Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 4.4e-06 (Fisher's exact test), Q value = 0.0017

Table S13. Gene #20: '10q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	79	110
10Q MUTATED	77	41	58
10Q WILD-TYPE	17	38	52

Figure S13. Get High-res Image Gene #20: '10q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.13e-05 (Fisher's exact test), Q value = 0.0083

Table S14. Gene #20: '10q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	122	87
10Q MUTATED	62	65	49
10Q WILD-TYPE	12	57	38

Figure S14. Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.043

Table S15. Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
11Q MUTATED	63	46	32
11Q WILD-TYPE	47	34	70

Figure S15. Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

'12p' versus 'CN_CNMF'

P value = 0.000449 (Fisher's exact test), Q value = 0.17

Table S16. Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
12P MUTATED	42	33	18
12P WILD-TYPE	68	47	84

Figure S16. Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'CN_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.089

Table S17. Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
13Q MUTATED	61	44	31
13Q WILD-TYPE	49	36	71

Figure S17. Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'14q' versus 'CN_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.013

Table S18. Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
14Q MUTATED	43	50	30
14Q WILD-TYPE	67	30	72

Figure S18. Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

'19p' versus 'CN_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.14

Table S19. Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
19P MUTATED	45	37	21
19P WILD-TYPE	65	43	81

Figure S19. Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.2

Table S20. Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
19Q MUTATED	45	36	21
19Q WILD-TYPE	65	44	81

Figure S20. Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'20p' versus 'CN_CNMF'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.0068

Table S21. Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
20P MUTATED	58	51	31
20P WILD-TYPE	52	29	71

Figure S21. Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.19

Table S22. Gene #36: '20p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	79	110
20P MUTATED	60	29	46
20P WILD-TYPE	34	50	64

Figure S22. Get High-res Image Gene #36: '20p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q' versus 'CN_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0059

Table S23. Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	80	102
20Q MUTATED	68	50	34
20Q WILD-TYPE	42	30	68

Figure S23. Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 1.43e-07 (Fisher's exact test), Q value = 5.7e-05

Table S24. Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	108	112
XQ MUTATED	32	53	18
XQ WILD-TYPE	40	55	94

Figure S24. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq' versus 'MRNASEQ_CNMF'

P value = 7.17e-05 (Fisher's exact test), Q value = 0.028

Table S25. Gene #40: 'xq' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	79	110
XQ MUTATED	42	13	46
XQ WILD-TYPE	52	66	64

Figure S25. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = SKCM-TM.transferedmergedcluster.txt
Number of patients = 292
Number of significantly focal cnvs = 40
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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