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

Uveal Melanoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_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 (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C14B30MZ

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, 97 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_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.3 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_1p36.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q27 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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_11q24.3 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.
del_16q12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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, 97 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 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.0001 (0.000246)	2e-05 (5.42e-05)
amp 8q24 22	61 (76%)	19	3e-05 (7.74e-05)	0.00013 (0.000315)	0.00387 (0.00784)	0.00065 (0.00142)	0.00257 (0.00534)	0.00056 (0.00126)	0.00017 (0.000406)	0.00042 (0.000974)
del 3p25 2	43 (54%)	37	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 3p25 1	43 (54%)	37	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 3p22 2	43 (54%)	37	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 3p14 2	44 (55%)	36	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 3q24	44 (55%)	36	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 3q29	44 (55%)	36	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 8p11 22	19 (24%)	61	1e-05 (2.81e-05)	7e-05 (0.000175)	3e-05 (7.74e-05)	1e-05 (2.81e-05)	3e-05 (7.74e-05)	1e-05 (2.81e-05)	2e-05 (5.42e-05)	6e-05 (0.000152)
del 16q24 3	17 (21%)	63	0.00111 (0.00237)	0.0158 (0.0287)	0.0488 (0.0805)	0.0046 (0.0092)	0.357 (0.406)	0.0387 (0.0652)	0.0812 (0.119)	0.00632 (0.012)
del 6q27	24 (30%)	56	0.00102 (0.00221)	0.0298 (0.0518)	0.111 (0.157)	0.00513 (0.01)	0.176 (0.227)	0.749 (0.778)	0.0518 (0.0837)	0.00381 (0.00782)
del 6q22 31	24 (30%)	56	0.00041 (0.000965)	0.0639 (0.1)	0.183 (0.232)	0.0147 (0.0271)	0.322 (0.373)	0.934 (0.946)	0.171 (0.223)	0.00117 (0.00246)
del 16q12 1	16 (20%)	64	0.0204 (0.0364)	0.132 (0.181)	0.0967 (0.138)	0.0128 (0.0238)	0.824 (0.845)	0.125 (0.172)	0.144 (0.193)	0.0463 (0.0771)
del 16q23 3	17 (21%)	63	0.00895 (0.0168)	0.0797 (0.119)	0.0502 (0.0819)	0.00485 (0.00958)	0.729 (0.763)	0.0965 (0.138)	0.0802 (0.119)	0.0302 (0.052)
amp 17q25 3	14 (18%)	66	0.206 (0.259)	0.0747 (0.113)	0.141 (0.191)	0.112 (0.157)	0.0059 (0.0114)	0.00058 (0.00129)	0.264 (0.32)	0.33 (0.38)
del 1p36 21	24 (30%)	56	0.00056 (0.00126)	0.0259 (0.0455)	0.427 (0.478)	0.165 (0.219)	0.518 (0.559)	0.474 (0.52)	0.304 (0.358)	0.491 (0.535)
del 11q24 3	7 (9%)	73	0.0668 (0.103)	0.0186 (0.0334)	0.0655 (0.102)	0.0742 (0.113)	0.0312 (0.0531)	0.146 (0.195)	1 (1.00)	0.522 (0.56)
del 2q37 2	3 (4%)	77	0.247 (0.302)	0.0549 (0.087)	0.297 (0.354)	0.236 (0.293)	0.313 (0.365)	0.443 (0.489)	0.299 (0.354)	0.69 (0.727)
del 5q23 1	4 (5%)	76	0.378 (0.426)	0.117 (0.162)	0.177 (0.227)	0.207 (0.259)	0.338 (0.387)	0.755 (0.78)	0.297 (0.354)	0.893 (0.91)
del 17q12	3 (4%)	77	0.247 (0.302)	0.0547 (0.087)	0.0893 (0.13)	0.169 (0.221)	0.596 (0.631)	0.44 (0.489)	0.593 (0.631)	0.94 (0.946)

'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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 = 2.8e-05

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 = 2.8e-05

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 = 2.8e-05

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 = 2.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
AMP PEAK 1(6P24.3) MUTATED	12	5	28
AMP PEAK 1(6P24.3) WILD-TYPE	22	12	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 = 2.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
AMP PEAK 1(6P24.3) MUTATED	4	9	27	5
AMP PEAK 1(6P24.3) WILD-TYPE	13	4	1	17

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 = 1e-04 (Fisher's exact test), Q value = 0.00025

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	28	14
AMP PEAK 1(6P24.3) MUTATED	12	24	5
AMP PEAK 1(6P24.3) WILD-TYPE	20	4	9

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 = 2e-05 (Fisher's exact test), Q value = 5.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
AMP PEAK 1(6P24.3) MUTATED	1	6	12	15	1	6
AMP PEAK 1(6P24.3) WILD-TYPE	4	6	4	1	14	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 = 3e-05 (Fisher's exact test), Q value = 7.7e-05

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 = 0.00013 (Fisher's exact test), Q value = 0.00032

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_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.0078

Table S11. Gene #2: 'amp_8q24.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
AMP PEAK 2(8Q24.22) MUTATED	28	12	21
AMP PEAK 2(8Q24.22) WILD-TYPE	2	3	14

Figure S11. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0014

Table S12. 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 S12. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0053

Table S13. Gene #2: 'amp_8q24.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
AMP PEAK 2(8Q24.22) MUTATED	32	10	19
AMP PEAK 2(8Q24.22) WILD-TYPE	2	7	10

Figure S13. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0013

Table S14. Gene #2: 'amp_8q24.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
AMP PEAK 2(8Q24.22) MUTATED	16	6	18	21
AMP PEAK 2(8Q24.22) WILD-TYPE	1	7	10	1

Figure S14. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00041

Table S15. Gene #2: 'amp_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	28	14
AMP PEAK 2(8Q24.22) MUTATED	31	15	12
AMP PEAK 2(8Q24.22) WILD-TYPE	1	13	2

Figure S15. 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 = 0.00042 (Fisher's exact test), Q value = 0.00097

Table S16. Gene #2: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
AMP PEAK 2(8Q24.22) MUTATED	5	11	6	12	14	10
AMP PEAK 2(8Q24.22) WILD-TYPE	0	1	10	4	1	0

Figure S16. Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.011

Table S17. Gene #3: 'amp_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
AMP PEAK 3(17Q25.3) MUTATED	4	0	10
AMP PEAK 3(17Q25.3) WILD-TYPE	30	17	19

Figure S17. Get High-res Image Gene #3: 'amp_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S18. Gene #3: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
AMP PEAK 3(17Q25.3) MUTATED	3	0	11	0
AMP PEAK 3(17Q25.3) WILD-TYPE	14	13	17	22

Figure S18. Get High-res Image Gene #3: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0013

Table S19. 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 S19. Get High-res Image Gene #4: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.046

Table S20. Gene #4: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 1(1P36.21) MUTATED	11	9	4
DEL PEAK 1(1P36.21) WILD-TYPE	22	9	25

Figure S20. Get High-res Image Gene #4: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S21. 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 S21. 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 = 2.8e-05

Table S22. 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 S22. 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 = 2.8e-05

Table S23. 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 S23. 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 = 2.8e-05

Table S24. 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 S24. 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 = 2.8e-05

Table S25. Gene #6: 'del_3p25.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
DEL PEAK 3(3P25.2) MUTATED	29	12	2
DEL PEAK 3(3P25.2) WILD-TYPE	5	5	27

Figure S25. 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 = 2.8e-05

Table S26. Gene #6: 'del_3p25.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
DEL PEAK 3(3P25.2) MUTATED	17	1	3	22
DEL PEAK 3(3P25.2) WILD-TYPE	0	12	25	0

Figure S26. 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 = 2.8e-05

Table S27. Gene #6: 'del_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	28	14
DEL PEAK 3(3P25.2) MUTATED	29	4	9
DEL PEAK 3(3P25.2) WILD-TYPE	3	24	5

Figure S27. 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 = 2.8e-05

Table S28. Gene #6: 'del_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 3(3P25.2) MUTATED	5	7	4	1	15	10
DEL PEAK 3(3P25.2) WILD-TYPE	0	5	12	15	0	0

Figure S28. 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 = 2.8e-05

Table S29. 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 S29. 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 = 2.8e-05

Table S30. 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 S30. 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 = 2.8e-05

Table S31. 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 S31. 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 = 2.8e-05

Table S32. 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 S32. 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 = 2.8e-05

Table S33. Gene #7: 'del_3p25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
DEL PEAK 4(3P25.1) MUTATED	29	12	2
DEL PEAK 4(3P25.1) WILD-TYPE	5	5	27

Figure S33. 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 = 2.8e-05

Table S34. Gene #7: 'del_3p25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
DEL PEAK 4(3P25.1) MUTATED	17	1	3	22
DEL PEAK 4(3P25.1) WILD-TYPE	0	12	25	0

Figure S34. 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 = 2.8e-05

Table S35. Gene #7: 'del_3p25.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	28	14
DEL PEAK 4(3P25.1) MUTATED	29	4	9
DEL PEAK 4(3P25.1) WILD-TYPE	3	24	5

Figure S35. 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 = 2.8e-05

Table S36. Gene #7: 'del_3p25.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 4(3P25.1) MUTATED	5	7	4	1	15	10
DEL PEAK 4(3P25.1) WILD-TYPE	0	5	12	15	0	0

Figure S36. 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 = 2.8e-05

Table S37. 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 S37. 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 = 2.8e-05

Table S38. 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 S38. 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 = 2.8e-05

Table S39. 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 S39. 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 = 2.8e-05

Table S40. 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 S40. 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 = 2.8e-05

Table S41. Gene #8: 'del_3p22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
DEL PEAK 5(3P22.2) MUTATED	29	12	2
DEL PEAK 5(3P22.2) WILD-TYPE	5	5	27

Figure S41. 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 = 2.8e-05

Table S42. Gene #8: 'del_3p22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
DEL PEAK 5(3P22.2) MUTATED	17	1	3	22
DEL PEAK 5(3P22.2) WILD-TYPE	0	12	25	0

Figure S42. 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 = 2.8e-05

Table S43. Gene #8: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	28	14
DEL PEAK 5(3P22.2) MUTATED	29	4	9
DEL PEAK 5(3P22.2) WILD-TYPE	3	24	5

Figure S43. 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 = 2.8e-05

Table S44. Gene #8: 'del_3p22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 5(3P22.2) MUTATED	5	7	4	1	15	10
DEL PEAK 5(3P22.2) WILD-TYPE	0	5	12	15	0	0

Figure S44. 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 = 2.8e-05

Table S45. 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 S45. 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 = 2.8e-05

Table S46. 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 S46. 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 = 2.8e-05

Table S47. 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 S47. 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 = 2.8e-05

Table S48. 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 S48. 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 = 2.8e-05

Table S49. Gene #9: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
DEL PEAK 6(3P14.2) MUTATED	30	12	2
DEL PEAK 6(3P14.2) WILD-TYPE	4	5	27

Figure S49. 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 = 2.8e-05

Table S50. Gene #9: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
DEL PEAK 6(3P14.2) MUTATED	17	2	3	22
DEL PEAK 6(3P14.2) WILD-TYPE	0	11	25	0

Figure S50. 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 = 2.8e-05

Table S51. Gene #9: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	28	14
DEL PEAK 6(3P14.2) MUTATED	30	4	9
DEL PEAK 6(3P14.2) WILD-TYPE	2	24	5

Figure S51. 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 = 2.8e-05

Table S52. Gene #9: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 6(3P14.2) MUTATED	5	8	4	1	15	10
DEL PEAK 6(3P14.2) WILD-TYPE	0	4	12	15	0	0

Figure S52. 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 = 2.8e-05

Table S53. 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 S53. 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 = 2.8e-05

Table S54. 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 S54. 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 = 2.8e-05

Table S55. 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 S55. 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 = 2.8e-05

Table S56. 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 S56. 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 = 2.8e-05

Table S57. Gene #10: 'del_3q24' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
DEL PEAK 7(3Q24) MUTATED	30	12	2
DEL PEAK 7(3Q24) WILD-TYPE	4	5	27

Figure S57. 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 = 2.8e-05

Table S58. Gene #10: 'del_3q24' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
DEL PEAK 7(3Q24) MUTATED	17	2	3	22
DEL PEAK 7(3Q24) WILD-TYPE	0	11	25	0

Figure S58. 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 = 2.8e-05

Table S59. Gene #10: 'del_3q24' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	28	14
DEL PEAK 7(3Q24) MUTATED	30	4	9
DEL PEAK 7(3Q24) WILD-TYPE	2	24	5

Figure S59. 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 = 2.8e-05

Table S60. Gene #10: 'del_3q24' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 7(3Q24) MUTATED	5	8	4	1	15	10
DEL PEAK 7(3Q24) WILD-TYPE	0	4	12	15	0	0

Figure S60. 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 = 2.8e-05

Table S61. 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 S61. 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 = 2.8e-05

Table S62. 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 S62. 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 = 2.8e-05

Table S63. 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 S63. 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 = 2.8e-05

Table S64. 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 S64. 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 = 2.8e-05

Table S65. Gene #11: 'del_3q29' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
DEL PEAK 8(3Q29) MUTATED	30	12	2
DEL PEAK 8(3Q29) WILD-TYPE	4	5	27

Figure S65. 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 = 2.8e-05

Table S66. Gene #11: 'del_3q29' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
DEL PEAK 8(3Q29) MUTATED	17	2	3	22
DEL PEAK 8(3Q29) WILD-TYPE	0	11	25	0

Figure S66. 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 = 2.8e-05

Table S67. Gene #11: 'del_3q29' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	28	14
DEL PEAK 8(3Q29) MUTATED	30	4	9
DEL PEAK 8(3Q29) WILD-TYPE	2	24	5

Figure S67. 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 = 2.8e-05

Table S68. Gene #11: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 8(3Q29) MUTATED	5	8	4	1	15	10
DEL PEAK 8(3Q29) WILD-TYPE	0	4	12	15	0	0

Figure S68. Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00096

Table S69. 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 S69. Get High-res Image Gene #13: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.027

Table S70. Gene #13: 'del_6q22.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 10(6Q22.31) MUTATED	13	10	1
DEL PEAK 10(6Q22.31) WILD-TYPE	16	23	17

Figure S70. Get High-res Image Gene #13: 'del_6q22.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.0025

Table S71. Gene #13: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 10(6Q22.31) MUTATED	3	2	2	7	2	8
DEL PEAK 10(6Q22.31) WILD-TYPE	2	10	14	9	13	2

Figure S71. Get High-res Image Gene #13: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0022

Table S72. 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 S72. Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.052

Table S73. Gene #14: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 11(6Q27) MUTATED	15	2	7
DEL PEAK 11(6Q27) WILD-TYPE	18	16	22

Figure S73. Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00513 (Fisher's exact test), Q value = 0.01

Table S74. Gene #14: 'del_6q27' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 11(6Q27) MUTATED	14	9	1
DEL PEAK 11(6Q27) WILD-TYPE	15	24	17

Figure S74. Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6q27' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.0078

Table S75. Gene #14: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 11(6Q27) MUTATED	3	2	2	6	3	8
DEL PEAK 11(6Q27) WILD-TYPE	2	10	14	10	12	2

Figure S75. Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S76. 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 S76. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.22' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00017

Table S77. 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 S77. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p11.22' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.7e-05

Table S78. 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 S78. 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 = 2.8e-05

Table S79. 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 S79. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.22' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.7e-05

Table S80. Gene #15: 'del_8p11.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
DEL PEAK 12(8P11.22) MUTATED	15	4	0
DEL PEAK 12(8P11.22) WILD-TYPE	19	13	29

Figure S80. 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 = 2.8e-05

Table S81. Gene #15: 'del_8p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
DEL PEAK 12(8P11.22) MUTATED	7	1	0	11
DEL PEAK 12(8P11.22) WILD-TYPE	10	12	28	11

Figure S81. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.4e-05

Table S82. Gene #15: 'del_8p11.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	28	14
DEL PEAK 12(8P11.22) MUTATED	16	0	3
DEL PEAK 12(8P11.22) WILD-TYPE	16	28	11

Figure S82. 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 = 6e-05 (Fisher's exact test), Q value = 0.00015

Table S83. Gene #15: 'del_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 12(8P11.22) MUTATED	3	4	0	0	7	5
DEL PEAK 12(8P11.22) WILD-TYPE	2	8	16	16	8	5

Figure S83. Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q24.3' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.033

Table S84. Gene #16: 'del_11q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 15(11Q24.3) MUTATED	1	0	6
DEL PEAK 15(11Q24.3) WILD-TYPE	32	18	23

Figure S84. Get High-res Image Gene #16: 'del_11q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q24.3' versus 'MIRSEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.053

Table S85. Gene #16: 'del_11q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	17	29
DEL PEAK 15(11Q24.3) MUTATED	1	0	6
DEL PEAK 15(11Q24.3) WILD-TYPE	33	17	23

Figure S85. Get High-res Image Gene #16: 'del_11q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16q12.1' versus 'CN_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.036

Table S86. Gene #17: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 16(16Q12.1) MUTATED	9	5	2
DEL PEAK 16(16Q12.1) WILD-TYPE	13	31	20

Figure S86. Get High-res Image Gene #17: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.024

Table S87. Gene #17: 'del_16q12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 16(16Q12.1) MUTATED	11	4	1
DEL PEAK 16(16Q12.1) WILD-TYPE	18	29	17

Figure S87. Get High-res Image Gene #17: 'del_16q12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.077

Table S88. Gene #17: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 16(16Q12.1) MUTATED	3	2	0	4	4	3
DEL PEAK 16(16Q12.1) WILD-TYPE	2	10	16	12	11	7

Figure S88. Get High-res Image Gene #17: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.00895 (Fisher's exact test), Q value = 0.017

Table S89. Gene #18: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	36	22
DEL PEAK 17(16Q23.3) MUTATED	10	5	2
DEL PEAK 17(16Q23.3) WILD-TYPE	12	31	20

Figure S89. Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00485 (Fisher's exact test), Q value = 0.0096

Table S90. Gene #18: 'del_16q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 17(16Q23.3) MUTATED	12	4	1
DEL PEAK 17(16Q23.3) WILD-TYPE	17	29	17

Figure S90. Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.052

Table S91. Gene #18: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 17(16Q23.3) MUTATED	3	2	0	4	4	4
DEL PEAK 17(16Q23.3) WILD-TYPE	2	10	16	12	11	6

Figure S91. Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.3' versus 'CN_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0024

Table S92. 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 S92. Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.3' versus 'METHLYATION_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.029

Table S93. Gene #19: 'del_16q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	29
DEL PEAK 18(16Q24.3) MUTATED	12	3	2
DEL PEAK 18(16Q24.3) WILD-TYPE	21	15	27

Figure S93. Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.081

Table S94. Gene #19: 'del_16q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	15	35
DEL PEAK 18(16Q24.3) MUTATED	11	2	4
DEL PEAK 18(16Q24.3) WILD-TYPE	19	13	31

Figure S94. Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.0092

Table S95. Gene #19: 'del_16q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	33	18
DEL PEAK 18(16Q24.3) MUTATED	12	4	1
DEL PEAK 18(16Q24.3) WILD-TYPE	17	29	17

Figure S95. Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0387 (Fisher's exact test), Q value = 0.065

Table S96. Gene #19: 'del_16q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	13	28	22
DEL PEAK 18(16Q24.3) MUTATED	6	0	4	7
DEL PEAK 18(16Q24.3) WILD-TYPE	11	13	24	15

Figure S96. Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00632 (Fisher's exact test), Q value = 0.012

Table S97. Gene #19: 'del_16q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	5	12	16	16	15	10
DEL PEAK 18(16Q24.3) MUTATED	3	1	0	4	4	5
DEL PEAK 18(16Q24.3) WILD-TYPE	2	11	16	12	11	5

Figure S97. Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/19783311/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/19785804/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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