Correlation between copy number variations of arm-level result and molecular subtypes

Brain Lower Grade Glioma (Primary solid tumor)

21 April 2013 | analyses__2013_04_21

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 (2013): Brain Lower Grade Glioma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C10C4SQ9

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 51 arm-level results and 8 molecular subtypes across 220 patients, 55 significant findings detected with Q value < 0.25.

1p gain cnv correlated to 'MRNASEQ_CNMF'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
19p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
1q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
4p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
4q loss cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.
10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
14q loss cnv correlated to 'METHLYATION_CNMF'.
19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
22q loss cnv correlated to 'CN_CNMF', '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 51 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 55 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
1p loss	0 (0%)	153	0.00361 (0.956)	0.00862 (1.00)	4.56e-47 (1.57e-44)	2.38e-51 (8.19e-49)	1.61e-24 (5.43e-22)	1.37e-30 (4.67e-28)	3.3e-14 (1.08e-11)	5.67e-07 (0.000182)
19q loss	0 (0%)	144	0.247 (1.00)	0.145 (1.00)	1.4e-45 (4.79e-43)	1.01e-36 (3.43e-34)	9.57e-22 (3.22e-19)	4.5e-27 (1.53e-24)	4.75e-13 (1.55e-10)	7.33e-07 (0.000234)
7p gain	0 (0%)	183	0.175 (1.00)	0.162 (1.00)	1.86e-17 (6.17e-15)	6.22e-11 (2.02e-08)	8.17e-12 (2.66e-09)	0.000204 (0.0605)	1.93e-05 (0.00601)	0.00221 (0.606)
7q gain	0 (0%)	169	0.282 (1.00)	0.144 (1.00)	6.78e-15 (2.23e-12)	2.14e-09 (6.93e-07)	6.56e-08 (2.12e-05)	0.00139 (0.39)	0.000112 (0.0337)	0.0586 (1.00)
20q gain	0 (0%)	204			8.04e-05 (0.0244)	5.24e-05 (0.0161)	7.35e-08 (2.37e-05)	0.0252 (1.00)	0.000833 (0.242)	0.0198 (1.00)
4p loss	0 (0%)	205	0.415 (1.00)	0.329 (1.00)	0.000882 (0.255)	0.000144 (0.043)	0.000108 (0.0324)	0.000418 (0.123)	1.41e-05 (0.00446)	0.397 (1.00)
19q gain	0 (0%)	211			0.00034 (0.1)	0.000707 (0.207)	0.000336 (0.0994)	0.0217 (1.00)	0.0422 (1.00)	0.104 (1.00)
20p gain	0 (0%)	203			1.66e-05 (0.00523)	7.69e-05 (0.0234)	1.7e-05 (0.00532)	0.259 (1.00)	0.0123 (1.00)	0.162 (1.00)
1q loss	0 (0%)	211	0.0889 (1.00)	0.0971 (1.00)	8.38e-05 (0.0253)	2.66e-05 (0.00822)	0.00603 (1.00)	0.00013 (0.039)	0.00694 (1.00)	0.506 (1.00)
10p loss	0 (0%)	189	0.271 (1.00)	0.241 (1.00)	2.3e-17 (7.62e-15)	2.62e-22 (8.84e-20)	4.79e-19 (1.59e-16)	0.0016 (0.447)	0.0111 (1.00)	0.00172 (0.478)
10q loss	0 (0%)	188	0.271 (1.00)	0.241 (1.00)	3.46e-16 (1.14e-13)	2.77e-21 (9.27e-19)	3.81e-20 (1.27e-17)	0.00109 (0.313)	0.00793 (1.00)	0.00468 (1.00)
22q loss	0 (0%)	205	1 (1.00)	0.763 (1.00)	7.15e-06 (0.00227)	6.34e-05 (0.0193)	1.92e-05 (0.00599)	0.0451 (1.00)	0.293 (1.00)	0.29 (1.00)
10p gain	0 (0%)	199			6.41e-07 (0.000205)	1.43e-05 (0.00451)	0.0175 (1.00)	0.094 (1.00)	0.873 (1.00)	0.921 (1.00)
19p gain	0 (0%)	209			2.25e-05 (0.00699)	5.91e-05 (0.0181)	0.00122 (0.345)	0.0102 (1.00)	0.0218 (1.00)	0.0177 (1.00)
4q loss	0 (0%)	196	0.839 (1.00)	0.828 (1.00)	0.0049 (1.00)	0.000399 (0.117)	0.002 (0.55)	0.00355 (0.945)	1.16e-06 (0.000369)	0.0589 (1.00)
1p gain	0 (0%)	214			0.0272 (1.00)	0.0843 (1.00)	3.39e-05 (0.0104)	0.103 (1.00)	0.391 (1.00)	0.114 (1.00)
14q loss	0 (0%)	196			0.00111 (0.316)	0.000835 (0.242)	0.00126 (0.356)	0.452 (1.00)	0.0696 (1.00)	0.112 (1.00)
1q gain	0 (0%)	212			0.00126 (0.356)	0.103 (1.00)	0.0312 (1.00)	0.618 (1.00)	0.918 (1.00)	0.368 (1.00)
6p gain	0 (0%)	216			0.213 (1.00)	0.427 (1.00)	0.0517 (1.00)	0.279 (1.00)	0.157 (1.00)	0.681 (1.00)
8p gain	0 (0%)	206			0.0337 (1.00)	0.235 (1.00)	0.606 (1.00)	0.464 (1.00)	0.0461 (1.00)	0.372 (1.00)
8q gain	0 (0%)	203			0.00467 (1.00)	0.0606 (1.00)	0.377 (1.00)	0.203 (1.00)	0.0606 (1.00)	0.339 (1.00)
9p gain	0 (0%)	216			0.213 (1.00)	0.543 (1.00)	0.0715 (1.00)	1 (1.00)	1 (1.00)	0.119 (1.00)
9q gain	0 (0%)	214			0.0272 (1.00)	0.273 (1.00)	0.00231 (0.63)	0.519 (1.00)	0.794 (1.00)	0.276 (1.00)
11p gain	0 (0%)	211			0.5 (1.00)	0.233 (1.00)	0.00395 (1.00)	0.00261 (0.701)	0.179 (1.00)	0.424 (1.00)
11q gain	0 (0%)	206			0.353 (1.00)	0.347 (1.00)	0.172 (1.00)	0.107 (1.00)	0.759 (1.00)	0.372 (1.00)
12p gain	0 (0%)	209			0.0368 (1.00)	0.106 (1.00)	0.286 (1.00)	0.17 (1.00)	0.0994 (1.00)	0.042 (1.00)
12q gain	0 (0%)	215			0.848 (1.00)	0.763 (1.00)	0.934 (1.00)	0.346 (1.00)	0.0533 (1.00)	0.118 (1.00)
18p gain	0 (0%)	216			0.213 (1.00)	0.543 (1.00)	0.569 (1.00)	0.279 (1.00)	0.469 (1.00)	0.173 (1.00)
21q gain	0 (0%)	217			0.328 (1.00)	0.6 (1.00)	0.158 (1.00)	0.0879 (1.00)	1 (1.00)	1 (1.00)
2p loss	0 (0%)	216			0.825 (1.00)	1 (1.00)	0.464 (1.00)	0.37 (1.00)	0.339 (1.00)	0.0404 (1.00)
2q loss	0 (0%)	217			0.796 (1.00)	1 (1.00)	0.513 (1.00)	0.259 (1.00)	0.0258 (1.00)	1 (1.00)
3p loss	0 (0%)	216			0.553 (1.00)	0.543 (1.00)	0.356 (1.00)	0.279 (1.00)	0.2 (1.00)	0.681 (1.00)
3q loss	0 (0%)	211	0.175 (1.00)	1 (1.00)	0.128 (1.00)	0.0699 (1.00)	0.547 (1.00)	0.453 (1.00)	0.869 (1.00)	1 (1.00)
5p loss	0 (0%)	209	1 (1.00)	0.388 (1.00)	0.0162 (1.00)	0.0233 (1.00)	0.847 (1.00)	0.36 (1.00)	0.0379 (1.00)	0.349 (1.00)
5q loss	0 (0%)	211	0.615 (1.00)	0.0971 (1.00)	0.0453 (1.00)	0.0699 (1.00)	0.0439 (1.00)	0.0217 (1.00)	0.00244 (0.66)	0.171 (1.00)
6p loss	0 (0%)	213			0.12 (1.00)	0.0239 (1.00)	0.139 (1.00)	1 (1.00)	0.501 (1.00)	0.106 (1.00)
6q loss	0 (0%)	199			0.00431 (1.00)	0.0122 (1.00)	0.362 (1.00)	0.332 (1.00)	0.206 (1.00)	0.337 (1.00)
8p loss	0 (0%)	217			0.17 (1.00)	0.167 (1.00)	0.571 (1.00)	1 (1.00)	0.0258 (1.00)	1 (1.00)
9p loss	0 (0%)	182	0.384 (1.00)	0.828 (1.00)	0.00289 (0.773)	0.0642 (1.00)	0.692 (1.00)	0.245 (1.00)	0.672 (1.00)	0.947 (1.00)
9q loss	0 (0%)	214			0.0702 (1.00)	0.0431 (1.00)	0.0111 (1.00)	0.000882 (0.255)	0.00498 (1.00)	0.531 (1.00)
11p loss	0 (0%)	200	0.815 (1.00)	0.526 (1.00)	0.00199 (0.55)	0.00111 (0.316)	0.0162 (1.00)	0.00897 (1.00)	0.00579 (1.00)	0.359 (1.00)
11q loss	0 (0%)	216			0.00243 (0.657)	0.177 (1.00)	0.00187 (0.518)	0.279 (1.00)	0.633 (1.00)	0.0404 (1.00)
12q loss	0 (0%)	212			0.0444 (1.00)	0.198 (1.00)	0.686 (1.00)	0.618 (1.00)	0.116 (1.00)	1 (1.00)
13q loss	0 (0%)	192	1 (1.00)	0.388 (1.00)	0.635 (1.00)	0.17 (1.00)	0.86 (1.00)	0.537 (1.00)	0.722 (1.00)	0.617 (1.00)
15q loss	0 (0%)	208			0.00582 (1.00)	0.00428 (1.00)	0.000977 (0.28)	0.00504 (1.00)	0.497 (1.00)	1 (1.00)
16q loss	0 (0%)	214			0.662 (1.00)	0.0843 (1.00)	0.302 (1.00)	0.519 (1.00)	0.713 (1.00)	0.755 (1.00)
18p loss	0 (0%)	205	0.344 (1.00)	0.413 (1.00)	0.144 (1.00)	0.0623 (1.00)	0.119 (1.00)	0.117 (1.00)	0.0756 (1.00)	0.125 (1.00)
18q loss	0 (0%)	204	0.0889 (1.00)	0.0971 (1.00)	0.00296 (0.789)	0.0055 (1.00)	0.0024 (0.652)	0.0264 (1.00)	0.109 (1.00)	0.236 (1.00)
19p loss	0 (0%)	210	0.302 (1.00)	0.0773 (1.00)	0.0618 (1.00)	0.149 (1.00)	0.0747 (1.00)	0.0204 (1.00)	0.0278 (1.00)	0.834 (1.00)
21q loss	0 (0%)	212			0.588 (1.00)	0.605 (1.00)	0.46 (1.00)	0.618 (1.00)	0.0647 (1.00)	0.00928 (1.00)
Xq loss	0 (0%)	214			0.132 (1.00)	0.35 (1.00)	0.698 (1.00)	0.103 (1.00)	0.0468 (1.00)	0.383 (1.00)

'1p gain' versus 'MRNASEQ_CNMF'

P value = 3.39e-05 (Chi-square test), Q value = 0.01

Table S1. Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
1P GAIN CNV	0	6	0	0	0
1P GAIN WILD-TYPE	60	36	35	70	11

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.86e-17 (Fisher's exact test), Q value = 6.2e-15

Table S2. Gene #4: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
7P GAIN CNV	5	30	2
7P GAIN WILD-TYPE	89	20	74

Figure S2. Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 6.22e-11 (Fisher's exact test), Q value = 2e-08

Table S3. Gene #4: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
7P GAIN CNV	12	21	2	1
7P GAIN WILD-TYPE	88	13	56	22

Figure S3. Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 8.17e-12 (Chi-square test), Q value = 2.7e-09

Table S4. Gene #4: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
7P GAIN CNV	10	23	2	2	0
7P GAIN WILD-TYPE	50	19	33	68	11

Figure S4. Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.061

Table S5. Gene #4: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
7P GAIN CNV	2	31	4
7P GAIN WILD-TYPE	30	86	65

Figure S5. Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.006

Table S6. Gene #4: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
7P GAIN CNV	17	1	5	14
7P GAIN WILD-TYPE	41	31	77	33

Figure S6. Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 6.78e-15 (Fisher's exact test), Q value = 2.2e-12

Table S7. Gene #5: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
7Q GAIN CNV	10	34	7
7Q GAIN WILD-TYPE	84	16	69

Figure S7. Get High-res Image Gene #5: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.14e-09 (Fisher's exact test), Q value = 6.9e-07

Table S8. Gene #5: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
7Q GAIN CNV	20	23	6	1
7Q GAIN WILD-TYPE	80	11	52	22

Figure S8. Get High-res Image Gene #5: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 6.56e-08 (Chi-square test), Q value = 2.1e-05

Table S9. Gene #5: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
7Q GAIN CNV	17	23	4	6	0
7Q GAIN WILD-TYPE	43	19	31	64	11

Figure S9. Get High-res Image Gene #5: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.034

Table S10. Gene #5: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
7Q GAIN CNV	19	2	11	19
7Q GAIN WILD-TYPE	39	30	71	28

Figure S10. Get High-res Image Gene #5: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 6.41e-07 (Fisher's exact test), Q value = 0.00021

Table S11. Gene #10: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
10P GAIN CNV	20	0	1
10P GAIN WILD-TYPE	74	50	75

Figure S11. Get High-res Image Gene #10: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.0045

Table S12. Gene #10: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
10P GAIN CNV	20	0	0	1
10P GAIN WILD-TYPE	80	34	58	22

Figure S12. Get High-res Image Gene #10: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.007

Table S13. Gene #16: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
19P GAIN CNV	2	9	0
19P GAIN WILD-TYPE	92	41	76

Figure S13. Get High-res Image Gene #16: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 5.91e-05 (Fisher's exact test), Q value = 0.018

Table S14. Gene #16: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
19P GAIN CNV	3	8	0	0
19P GAIN WILD-TYPE	97	26	58	23

Figure S14. Get High-res Image Gene #16: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.1

Table S15. Gene #17: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
19Q GAIN CNV	2	7	0
19Q GAIN WILD-TYPE	92	43	76

Figure S15. Get High-res Image Gene #17: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.000707 (Fisher's exact test), Q value = 0.21

Table S16. Gene #17: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
19Q GAIN CNV	2	6	0	0
19Q GAIN WILD-TYPE	98	28	58	23

Figure S16. Get High-res Image Gene #17: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.000336 (Chi-square test), Q value = 0.099

Table S17. Gene #17: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
19Q GAIN CNV	1	7	0	1	0
19Q GAIN WILD-TYPE	59	35	35	69	11

Figure S17. Get High-res Image Gene #17: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.0052

Table S18. Gene #18: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
20P GAIN CNV	4	12	1
20P GAIN WILD-TYPE	90	38	75

Figure S18. Get High-res Image Gene #18: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 7.69e-05 (Fisher's exact test), Q value = 0.023

Table S19. Gene #18: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
20P GAIN CNV	6	10	1	0
20P GAIN WILD-TYPE	94	24	57	23

Figure S19. Get High-res Image Gene #18: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1.7e-05 (Chi-square test), Q value = 0.0053

Table S20. Gene #18: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
20P GAIN CNV	2	11	1	2	0
20P GAIN WILD-TYPE	58	31	34	68	11

Figure S20. Get High-res Image Gene #18: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 8.04e-05 (Fisher's exact test), Q value = 0.024

Table S21. Gene #19: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
20Q GAIN CNV	4	11	1
20Q GAIN WILD-TYPE	90	39	75

Figure S21. Get High-res Image Gene #19: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5.24e-05 (Fisher's exact test), Q value = 0.016

Table S22. Gene #19: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
20Q GAIN CNV	5	10	1	0
20Q GAIN WILD-TYPE	95	24	57	23

Figure S22. Get High-res Image Gene #19: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 7.35e-08 (Chi-square test), Q value = 2.4e-05

Table S23. Gene #19: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
20Q GAIN CNV	2	12	1	0	0
20Q GAIN WILD-TYPE	58	30	34	70	11

Figure S23. Get High-res Image Gene #19: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.000833 (Fisher's exact test), Q value = 0.24

Table S24. Gene #19: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
20Q GAIN CNV	8	0	1	7
20Q GAIN WILD-TYPE	50	32	81	40

Figure S24. Get High-res Image Gene #19: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 4.56e-47 (Fisher's exact test), Q value = 1.6e-44

Table S25. Gene #21: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
1P LOSS CNV	0	0	67
1P LOSS WILD-TYPE	94	50	9

Figure S25. Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 2.38e-51 (Fisher's exact test), Q value = 8.2e-49

Table S26. Gene #21: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
1P LOSS CNV	0	0	58	6
1P LOSS WILD-TYPE	100	34	0	17

Figure S26. Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.61e-24 (Chi-square test), Q value = 5.4e-22

Table S27. Gene #21: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
1P LOSS CNV	0	0	33	31	3
1P LOSS WILD-TYPE	60	42	2	39	8

Figure S27. Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-30 (Fisher's exact test), Q value = 4.7e-28

Table S28. Gene #21: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
1P LOSS CNV	32	4	31
1P LOSS WILD-TYPE	0	113	38

Figure S28. Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 3.3e-14 (Fisher's exact test), Q value = 1.1e-11

Table S29. Gene #21: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
1P LOSS CNV	6	21	39	1
1P LOSS WILD-TYPE	52	11	43	46

Figure S29. Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.67e-07 (Fisher's exact test), Q value = 0.00018

Table S30. Gene #21: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	95	116
1P LOSS CNV	3	46	18
1P LOSS WILD-TYPE	5	49	98

Figure S30. Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 8.38e-05 (Fisher's exact test), Q value = 0.025

Table S31. Gene #22: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
1Q LOSS CNV	0	0	9
1Q LOSS WILD-TYPE	94	50	67

Figure S31. Get High-res Image Gene #22: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.0082

Table S32. Gene #22: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
1Q LOSS CNV	0	0	9	0
1Q LOSS WILD-TYPE	100	34	49	23

Figure S32. Get High-res Image Gene #22: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.039

Table S33. Gene #22: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
1Q LOSS CNV	5	0	4
1Q LOSS WILD-TYPE	27	117	65

Figure S33. Get High-res Image Gene #22: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.043

Table S34. Gene #27: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
4P LOSS CNV	3	0	12	0
4P LOSS WILD-TYPE	97	34	46	23

Figure S34. Get High-res Image Gene #27: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.000108 (Chi-square test), Q value = 0.032

Table S35. Gene #27: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
4P LOSS CNV	0	0	8	7	0
4P LOSS WILD-TYPE	60	42	27	63	11

Figure S35. Get High-res Image Gene #27: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000418 (Fisher's exact test), Q value = 0.12

Table S36. Gene #27: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
4P LOSS CNV	7	2	6
4P LOSS WILD-TYPE	25	115	63

Figure S36. Get High-res Image Gene #27: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0045

Table S37. Gene #27: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
4P LOSS CNV	0	9	5	1
4P LOSS WILD-TYPE	58	23	77	46

Figure S37. Get High-res Image Gene #27: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.000399 (Fisher's exact test), Q value = 0.12

Table S38. Gene #28: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
4Q LOSS CNV	8	0	15	1
4Q LOSS WILD-TYPE	92	34	43	22

Figure S38. Get High-res Image Gene #28: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00037

Table S39. Gene #28: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
4Q LOSS CNV	1	13	8	2
4Q LOSS WILD-TYPE	57	19	74	45

Figure S39. Get High-res Image Gene #28: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 2.3e-17 (Fisher's exact test), Q value = 7.6e-15

Table S40. Gene #36: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
10P LOSS CNV	1	27	3
10P LOSS WILD-TYPE	93	23	73

Figure S40. Get High-res Image Gene #36: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 2.62e-22 (Fisher's exact test), Q value = 8.8e-20

Table S41. Gene #36: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
10P LOSS CNV	1	26	3	0
10P LOSS WILD-TYPE	99	8	55	23

Figure S41. Get High-res Image Gene #36: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 4.79e-19 (Chi-square test), Q value = 1.6e-16

Table S42. Gene #36: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
10P LOSS CNV	1	25	1	3	0
10P LOSS WILD-TYPE	59	17	34	67	11

Figure S42. Get High-res Image Gene #36: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 3.46e-16 (Fisher's exact test), Q value = 1.1e-13

Table S43. Gene #37: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
10Q LOSS CNV	2	27	3
10Q LOSS WILD-TYPE	92	23	73

Figure S43. Get High-res Image Gene #37: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 2.77e-21 (Fisher's exact test), Q value = 9.3e-19

Table S44. Gene #37: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
10Q LOSS CNV	2	26	3	0
10Q LOSS WILD-TYPE	98	8	55	23

Figure S44. Get High-res Image Gene #37: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 3.81e-20 (Chi-square test), Q value = 1.3e-17

Table S45. Gene #37: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
10Q LOSS CNV	1	26	1	3	0
10Q LOSS WILD-TYPE	59	16	34	67	11

Figure S45. Get High-res Image Gene #37: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.000835 (Fisher's exact test), Q value = 0.24

Table S46. Gene #42: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
14Q LOSS CNV	8	11	5	0
14Q LOSS WILD-TYPE	92	23	53	23

Figure S46. Get High-res Image Gene #42: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1.4e-45 (Fisher's exact test), Q value = 4.8e-43

Table S47. Gene #48: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
19Q LOSS CNV	2	3	71
19Q LOSS WILD-TYPE	92	47	5

Figure S47. Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1.01e-36 (Fisher's exact test), Q value = 3.4e-34

Table S48. Gene #48: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
19Q LOSS CNV	8	2	57	6
19Q LOSS WILD-TYPE	92	32	1	17

Figure S48. Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 9.57e-22 (Chi-square test), Q value = 3.2e-19

Table S49. Gene #48: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
19Q LOSS CNV	4	1	33	36	2
19Q LOSS WILD-TYPE	56	41	2	34	9

Figure S49. Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.5e-27 (Fisher's exact test), Q value = 1.5e-24

Table S50. Gene #48: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
19Q LOSS CNV	32	9	35
19Q LOSS WILD-TYPE	0	108	34

Figure S50. Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 4.75e-13 (Fisher's exact test), Q value = 1.6e-10

Table S51. Gene #48: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
19Q LOSS CNV	7	23	42	4
19Q LOSS WILD-TYPE	51	9	40	43

Figure S51. Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.33e-07 (Fisher's exact test), Q value = 0.00023

Table S52. Gene #48: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	95	116
19Q LOSS CNV	2	51	23
19Q LOSS WILD-TYPE	6	44	93

Figure S52. Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 7.15e-06 (Fisher's exact test), Q value = 0.0023

Table S53. Gene #50: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
22Q LOSS CNV	4	11	0
22Q LOSS WILD-TYPE	90	39	76

Figure S53. Get High-res Image Gene #50: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 6.34e-05 (Fisher's exact test), Q value = 0.019

Table S54. Gene #50: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
22Q LOSS CNV	6	9	0	0
22Q LOSS WILD-TYPE	94	25	58	23

Figure S54. Get High-res Image Gene #50: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1.92e-05 (Chi-square test), Q value = 0.006

Table S55. Gene #50: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
22Q LOSS CNV	1	10	0	3	0
22Q LOSS WILD-TYPE	59	32	35	67	11

Figure S55. Get High-res Image Gene #50: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

Methods & Data

Input

Mutation data file = broad_values_by_arm.mutsig.cluster.txt
Molecular subtypes file = LGG-TP.transferedmergedcluster.txt
Number of patients = 220
Number of significantly arm-level cnvs = 51
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have mutations, 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] 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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