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

Uveal Melanoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C1ST7NTR

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 20 focal events and 8 molecular subtypes across 80 patients, 76 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_6p24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.3 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
del_1p36.21 cnv correlated to 'CN_CNMF'.
del_3p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q24 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q29 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'CN_CNMF'.
del_6q27 cnv correlated to 'CN_CNMF'.
del_8p11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.3 cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 20 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 76 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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
amp 6p24 3	45 (56%)	35	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	6e-05 (0.00576)	1e-05 (0.0016)
del 3p25 2	43 (54%)	37	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)
del 3p25 1	43 (54%)	37	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)
del 3p22 2	43 (54%)	37	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)
del 3p14 2	44 (55%)	36	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)
del 3q24	44 (55%)	36	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)
del 3q29	44 (55%)	36	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)	1e-05 (0.0016)
del 8p11 22	19 (24%)	61	1e-05 (0.0016)	3e-05 (0.00297)	4e-05 (0.00392)	1e-05 (0.0016)	6e-05 (0.00576)	1e-05 (0.0016)	1e-05 (0.0016)	2e-05 (0.002)
amp 8q24 22	61 (76%)	19	5e-05 (0.00485)	0.00018 (0.0169)	0.00443 (0.372)	0.00082 (0.0746)	0.00212 (0.18)	0.00116 (0.101)	1e-05 (0.0016)	0.00102 (0.0908)
amp 17q25 3	14 (18%)	66	0.208 (1.00)	0.0736 (1.00)	0.142 (1.00)	0.114 (1.00)	0.00606 (0.485)	0.00157 (0.135)	0.153 (1.00)	0.0972 (1.00)
del 1p36 21	24 (30%)	56	0.00057 (0.0524)	0.0265 (1.00)	0.429 (1.00)	0.168 (1.00)	0.39 (1.00)	0.00643 (0.502)	0.265 (1.00)	0.244 (1.00)
del 6q22 31	24 (30%)	56	0.00033 (0.0307)	0.0615 (1.00)	0.183 (1.00)	0.0147 (1.00)	0.373 (1.00)	0.758 (1.00)	0.098 (1.00)	0.0107 (0.806)
del 6q27	24 (30%)	56	0.00094 (0.0846)	0.0292 (1.00)	0.111 (1.00)	0.00491 (0.398)	0.211 (1.00)	0.574 (1.00)	0.0228 (1.00)	0.01 (0.764)
del 16q24 3	17 (21%)	63	0.00112 (0.0986)	0.0163 (1.00)	0.0509 (1.00)	0.00477 (0.396)	0.332 (1.00)	0.0237 (1.00)	0.0872 (1.00)	0.0324 (1.00)
del 2q37 2	3 (4%)	77	0.247 (1.00)	0.0552 (1.00)	0.297 (1.00)	0.234 (1.00)	0.306 (1.00)	0.393 (1.00)	0.204 (1.00)	0.437 (1.00)
del 5q23 1	4 (5%)	76	0.377 (1.00)	0.115 (1.00)	0.177 (1.00)	0.208 (1.00)	0.413 (1.00)	0.289 (1.00)	0.206 (1.00)	0.838 (1.00)
del 11q24 3	7 (9%)	73	0.0678 (1.00)	0.0185 (1.00)	0.0682 (1.00)	0.0737 (1.00)	0.0291 (1.00)	0.119 (1.00)	0.469 (1.00)	0.176 (1.00)
del 16q12 1	16 (20%)	64	0.0213 (1.00)	0.133 (1.00)	0.0957 (1.00)	0.0131 (0.969)	0.934 (1.00)	0.00606 (0.485)	0.359 (1.00)	0.239 (1.00)
del 16q23 3	17 (21%)	63	0.0088 (0.678)	0.0779 (1.00)	0.0504 (1.00)	0.00482 (0.396)	0.729 (1.00)	0.0136 (0.995)	0.263 (1.00)	0.133 (1.00)
del 17q12	3 (4%)	77	0.249 (1.00)	0.0538 (1.00)	0.087 (1.00)	0.172 (1.00)	0.594 (1.00)	0.0703 (1.00)	0.127 (1.00)	0.527 (1.00)

'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S1. Gene #1: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
AMP PEAK 1(6P24.3) MUTATED	9	32	4
AMP PEAK 1(6P24.3) WILD-TYPE	13	4	18

Figure S1. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S2. Gene #1: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
AMP PEAK 1(6P24.3) MUTATED	10	8	27
AMP PEAK 1(6P24.3) WILD-TYPE	23	10	2

Figure S2. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S3. Gene #1: 'amp_6p24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
AMP PEAK 1(6P24.3) MUTATED	8	6	31
AMP PEAK 1(6P24.3) WILD-TYPE	22	9	4

Figure S3. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S4. Gene #1: 'amp_6p24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
AMP PEAK 1(6P24.3) MUTATED	9	30	6
AMP PEAK 1(6P24.3) WILD-TYPE	20	3	12

Figure S4. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S5. Gene #1: 'amp_6p24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	16	29
AMP PEAK 1(6P24.3) MUTATED	11	5	28
AMP PEAK 1(6P24.3) WILD-TYPE	23	11	1

Figure S5. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S6. Gene #1: 'amp_6p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
AMP PEAK 1(6P24.3) MUTATED	2	8	18	5	9	2
AMP PEAK 1(6P24.3) WILD-TYPE	6	4	0	19	1	5

Figure S6. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0058

Table S7. Gene #1: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	29	12
AMP PEAK 1(6P24.3) MUTATED	11	25	4
AMP PEAK 1(6P24.3) WILD-TYPE	21	4	8

Figure S7. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S8. Gene #1: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	11	32	10
AMP PEAK 1(6P24.3) MUTATED	2	5	27	6
AMP PEAK 1(6P24.3) WILD-TYPE	18	6	5	4

Figure S8. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0048

Table S9. Gene #2: 'amp_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
AMP PEAK 2(8Q24.22) MUTATED	22	19	20
AMP PEAK 2(8Q24.22) WILD-TYPE	0	17	2

Figure S9. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.017

Table S10. Gene #2: 'amp_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
AMP PEAK 2(8Q24.22) MUTATED	32	13	16
AMP PEAK 2(8Q24.22) WILD-TYPE	1	5	13

Figure S10. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.075

Table S11. Gene #2: 'amp_8q24.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
AMP PEAK 2(8Q24.22) MUTATED	28	19	14
AMP PEAK 2(8Q24.22) WILD-TYPE	1	14	4

Figure S11. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.18

Table S12. Gene #2: 'amp_8q24.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	16	29
AMP PEAK 2(8Q24.22) MUTATED	32	9	19
AMP PEAK 2(8Q24.22) WILD-TYPE	2	7	10

Figure S12. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.1

Table S13. Gene #2: 'amp_8q24.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
AMP PEAK 2(8Q24.22) MUTATED	8	5	12	23	6	6
AMP PEAK 2(8Q24.22) WILD-TYPE	0	7	6	1	4	1

Figure S13. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S14. Gene #2: 'amp_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	29	12
AMP PEAK 2(8Q24.22) MUTATED	32	15	10
AMP PEAK 2(8Q24.22) WILD-TYPE	0	14	2

Figure S14. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.091

Table S15. Gene #2: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	11	32	10
AMP PEAK 2(8Q24.22) MUTATED	19	10	18	10
AMP PEAK 2(8Q24.22) WILD-TYPE	1	1	14	0

Figure S15. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.14

Table S16. Gene #3: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
AMP PEAK 3(17Q25.3) MUTATED	0	0	6	1	5	2
AMP PEAK 3(17Q25.3) WILD-TYPE	8	12	12	23	5	5

Figure S16. Get High-res Image Gene #3: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.052

Table S17. Gene #4: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 1(1P36.21) MUTATED	4	6	14
DEL PEAK 1(1P36.21) WILD-TYPE	18	30	8

Figure S17. Get High-res Image Gene #4: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S18. Gene #6: 'del_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 3(3P25.2) MUTATED	22	2	19
DEL PEAK 3(3P25.2) WILD-TYPE	0	34	3

Figure S18. Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p25.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S19. Gene #6: 'del_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 3(3P25.2) MUTATED	33	9	1
DEL PEAK 3(3P25.2) WILD-TYPE	0	9	28

Figure S19. Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S20. Gene #6: 'del_3p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
DEL PEAK 3(3P25.2) MUTATED	30	10	3
DEL PEAK 3(3P25.2) WILD-TYPE	0	5	32

Figure S20. Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S21. Gene #6: 'del_3p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 3(3P25.2) MUTATED	29	2	12
DEL PEAK 3(3P25.2) WILD-TYPE	0	31	6

Figure S21. Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S22. Gene #6: 'del_3p25.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	16	29
DEL PEAK 3(3P25.2) MUTATED	30	11	2
DEL PEAK 3(3P25.2) WILD-TYPE	4	5	27

Figure S22. Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S23. Gene #6: 'del_3p25.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
DEL PEAK 3(3P25.2) MUTATED	8	1	1	24	2	7
DEL PEAK 3(3P25.2) WILD-TYPE	0	11	17	0	8	0

Figure S23. Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S24. Gene #6: 'del_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	29	12
DEL PEAK 3(3P25.2) MUTATED	30	4	8
DEL PEAK 3(3P25.2) WILD-TYPE	2	25	4

Figure S24. Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S25. Gene #6: 'del_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	11	32	10
DEL PEAK 3(3P25.2) MUTATED	20	7	5	10
DEL PEAK 3(3P25.2) WILD-TYPE	0	4	27	0

Figure S25. Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S26. Gene #7: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 4(3P25.1) MUTATED	22	2	19
DEL PEAK 4(3P25.1) WILD-TYPE	0	34	3

Figure S26. Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S27. Gene #7: 'del_3p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 4(3P25.1) MUTATED	33	9	1
DEL PEAK 4(3P25.1) WILD-TYPE	0	9	28

Figure S27. Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S28. Gene #7: 'del_3p25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
DEL PEAK 4(3P25.1) MUTATED	30	10	3
DEL PEAK 4(3P25.1) WILD-TYPE	0	5	32

Figure S28. Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S29. Gene #7: 'del_3p25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 4(3P25.1) MUTATED	29	2	12
DEL PEAK 4(3P25.1) WILD-TYPE	0	31	6

Figure S29. Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S30. Gene #7: 'del_3p25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	16	29
DEL PEAK 4(3P25.1) MUTATED	30	11	2
DEL PEAK 4(3P25.1) WILD-TYPE	4	5	27

Figure S30. Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S31. Gene #7: 'del_3p25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
DEL PEAK 4(3P25.1) MUTATED	8	1	1	24	2	7
DEL PEAK 4(3P25.1) WILD-TYPE	0	11	17	0	8	0

Figure S31. Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S32. Gene #7: 'del_3p25.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	29	12
DEL PEAK 4(3P25.1) MUTATED	30	4	8
DEL PEAK 4(3P25.1) WILD-TYPE	2	25	4

Figure S32. Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S33. Gene #7: 'del_3p25.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	11	32	10
DEL PEAK 4(3P25.1) MUTATED	20	7	5	10
DEL PEAK 4(3P25.1) WILD-TYPE	0	4	27	0

Figure S33. Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S34. Gene #8: 'del_3p22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 5(3P22.2) MUTATED	22	2	19
DEL PEAK 5(3P22.2) WILD-TYPE	0	34	3

Figure S34. Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S35. Gene #8: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 5(3P22.2) MUTATED	33	9	1
DEL PEAK 5(3P22.2) WILD-TYPE	0	9	28

Figure S35. Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S36. Gene #8: 'del_3p22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
DEL PEAK 5(3P22.2) MUTATED	30	10	3
DEL PEAK 5(3P22.2) WILD-TYPE	0	5	32

Figure S36. Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S37. Gene #8: 'del_3p22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 5(3P22.2) MUTATED	29	2	12
DEL PEAK 5(3P22.2) WILD-TYPE	0	31	6

Figure S37. Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S38. Gene #8: 'del_3p22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	16	29
DEL PEAK 5(3P22.2) MUTATED	30	11	2
DEL PEAK 5(3P22.2) WILD-TYPE	4	5	27

Figure S38. Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S39. Gene #8: 'del_3p22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
DEL PEAK 5(3P22.2) MUTATED	8	1	1	24	2	7
DEL PEAK 5(3P22.2) WILD-TYPE	0	11	17	0	8	0

Figure S39. Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S40. Gene #8: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	29	12
DEL PEAK 5(3P22.2) MUTATED	30	4	8
DEL PEAK 5(3P22.2) WILD-TYPE	2	25	4

Figure S40. Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S41. Gene #8: 'del_3p22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	11	32	10
DEL PEAK 5(3P22.2) MUTATED	20	7	5	10
DEL PEAK 5(3P22.2) WILD-TYPE	0	4	27	0

Figure S41. Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S42. Gene #9: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 6(3P14.2) MUTATED	22	2	20
DEL PEAK 6(3P14.2) WILD-TYPE	0	34	2

Figure S42. Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S43. Gene #9: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 6(3P14.2) MUTATED	33	10	1
DEL PEAK 6(3P14.2) WILD-TYPE	0	8	28

Figure S43. Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S44. Gene #9: 'del_3p14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
DEL PEAK 6(3P14.2) MUTATED	30	10	4
DEL PEAK 6(3P14.2) WILD-TYPE	0	5	31

Figure S44. Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S45. Gene #9: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 6(3P14.2) MUTATED	29	2	13
DEL PEAK 6(3P14.2) WILD-TYPE	0	31	5

Figure S45. Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S46. Gene #9: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	16	29
DEL PEAK 6(3P14.2) MUTATED	31	11	2
DEL PEAK 6(3P14.2) WILD-TYPE	3	5	27

Figure S46. Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S47. Gene #9: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
DEL PEAK 6(3P14.2) MUTATED	8	2	1	24	2	7
DEL PEAK 6(3P14.2) WILD-TYPE	0	10	17	0	8	0

Figure S47. Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S48. Gene #9: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	29	12
DEL PEAK 6(3P14.2) MUTATED	31	4	8
DEL PEAK 6(3P14.2) WILD-TYPE	1	25	4

Figure S48. Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S49. Gene #9: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	11	32	10
DEL PEAK 6(3P14.2) MUTATED	20	8	5	10
DEL PEAK 6(3P14.2) WILD-TYPE	0	3	27	0

Figure S49. Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q24' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S50. Gene #10: 'del_3q24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 7(3Q24) MUTATED	22	2	20
DEL PEAK 7(3Q24) WILD-TYPE	0	34	2

Figure S50. Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q24' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S51. Gene #10: 'del_3q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 7(3Q24) MUTATED	33	10	1
DEL PEAK 7(3Q24) WILD-TYPE	0	8	28

Figure S51. Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q24' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S52. Gene #10: 'del_3q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
DEL PEAK 7(3Q24) MUTATED	30	10	4
DEL PEAK 7(3Q24) WILD-TYPE	0	5	31

Figure S52. Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3q24' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S53. Gene #10: 'del_3q24' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 7(3Q24) MUTATED	29	2	13
DEL PEAK 7(3Q24) WILD-TYPE	0	31	5

Figure S53. Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3q24' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S54. Gene #10: 'del_3q24' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	16	29
DEL PEAK 7(3Q24) MUTATED	31	11	2
DEL PEAK 7(3Q24) WILD-TYPE	3	5	27

Figure S54. Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3q24' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S55. Gene #10: 'del_3q24' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
DEL PEAK 7(3Q24) MUTATED	8	2	1	24	2	7
DEL PEAK 7(3Q24) WILD-TYPE	0	10	17	0	8	0

Figure S55. Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q24' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S56. Gene #10: 'del_3q24' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	29	12
DEL PEAK 7(3Q24) MUTATED	31	4	8
DEL PEAK 7(3Q24) WILD-TYPE	1	25	4

Figure S56. Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3q24' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S57. Gene #10: 'del_3q24' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	11	32	10
DEL PEAK 7(3Q24) MUTATED	20	8	5	10
DEL PEAK 7(3Q24) WILD-TYPE	0	3	27	0

Figure S57. Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S58. Gene #11: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 8(3Q29) MUTATED	22	2	20
DEL PEAK 8(3Q29) WILD-TYPE	0	34	2

Figure S58. Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S59. Gene #11: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 8(3Q29) MUTATED	33	10	1
DEL PEAK 8(3Q29) WILD-TYPE	0	8	28

Figure S59. Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S60. Gene #11: 'del_3q29' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
DEL PEAK 8(3Q29) MUTATED	30	10	4
DEL PEAK 8(3Q29) WILD-TYPE	0	5	31

Figure S60. Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S61. Gene #11: 'del_3q29' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 8(3Q29) MUTATED	29	2	13
DEL PEAK 8(3Q29) WILD-TYPE	0	31	5

Figure S61. Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S62. Gene #11: 'del_3q29' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	16	29
DEL PEAK 8(3Q29) MUTATED	31	11	2
DEL PEAK 8(3Q29) WILD-TYPE	3	5	27

Figure S62. Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S63. Gene #11: 'del_3q29' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
DEL PEAK 8(3Q29) MUTATED	8	2	1	24	2	7
DEL PEAK 8(3Q29) WILD-TYPE	0	10	17	0	8	0

Figure S63. Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S64. Gene #11: 'del_3q29' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	29	12
DEL PEAK 8(3Q29) MUTATED	31	4	8
DEL PEAK 8(3Q29) WILD-TYPE	1	25	4

Figure S64. Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3q29' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S65. Gene #11: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	11	32	10
DEL PEAK 8(3Q29) MUTATED	20	8	5	10
DEL PEAK 8(3Q29) WILD-TYPE	0	3	27	0

Figure S65. Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.031

Table S66. Gene #13: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 10(6Q22.31) MUTATED	13	10	1
DEL PEAK 10(6Q22.31) WILD-TYPE	9	26	21

Figure S66. Get High-res Image Gene #13: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.085

Table S67. Gene #14: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 11(6Q27) MUTATED	13	9	2
DEL PEAK 11(6Q27) WILD-TYPE	9	27	20

Figure S67. Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S68. Gene #15: 'del_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 12(8P11.22) MUTATED	16	1	2
DEL PEAK 12(8P11.22) WILD-TYPE	6	35	20

Figure S68. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.22' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.003

Table S69. Gene #15: 'del_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 12(8P11.22) MUTATED	16	2	1
DEL PEAK 12(8P11.22) WILD-TYPE	17	16	28

Figure S69. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p11.22' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0039

Table S70. Gene #15: 'del_8p11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
DEL PEAK 12(8P11.22) MUTATED	15	3	1
DEL PEAK 12(8P11.22) WILD-TYPE	15	12	34

Figure S70. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_8p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S71. Gene #15: 'del_8p11.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 12(8P11.22) MUTATED	16	1	2
DEL PEAK 12(8P11.22) WILD-TYPE	13	32	16

Figure S71. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.22' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0058

Table S72. Gene #15: 'del_8p11.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	16	29
DEL PEAK 12(8P11.22) MUTATED	15	4	0
DEL PEAK 12(8P11.22) WILD-TYPE	19	12	29

Figure S72. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_8p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S73. Gene #15: 'del_8p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	12	18	24	10	7
DEL PEAK 12(8P11.22) MUTATED	6	1	0	12	0	0
DEL PEAK 12(8P11.22) WILD-TYPE	2	11	18	12	10	7

Figure S73. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S74. Gene #15: 'del_8p11.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	29	12
DEL PEAK 12(8P11.22) MUTATED	17	0	2
DEL PEAK 12(8P11.22) WILD-TYPE	15	29	10

Figure S74. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_8p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.002

Table S75. Gene #15: 'del_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	11	32	10
DEL PEAK 12(8P11.22) MUTATED	10	4	0	5
DEL PEAK 12(8P11.22) WILD-TYPE	10	7	32	5

Figure S75. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.3' versus 'CN_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.099

Table S76. Gene #19: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 18(16Q24.3) MUTATED	11	4	2
DEL PEAK 18(16Q24.3) WILD-TYPE	11	32	20

Figure S76. Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = UVM-TP.transferedmergedcluster.txt
Number of patients = 80
Number of significantly focal cnvs = 20
Number of molecular subtypes = 8
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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