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

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 12 focal events and 10 molecular subtypes across 123 patients, 69 significant findings detected with P value < 0.05 and Q value < 0.25.

del_2q37.1 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.3 cnv correlated to 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q22.33 cnv correlated to 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.11 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_22q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 12 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 69 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 6p25 2	26 (21%)	97	1e-05 (1e-04)	1e-05 (1e-04)	2e-05 (0.000141)	0.00023 (0.00106)	0.00173 (0.00649)	4e-05 (0.00024)	0.0012 (0.0048)	0.00654 (0.0196)	2e-05 (0.000141)	0.00491 (0.0155)
del 6q21	20 (16%)	103	1e-05 (1e-04)	1e-05 (1e-04)	1e-05 (1e-04)	3e-05 (0.000189)	1e-05 (1e-04)	1e-05 (1e-04)	2e-05 (0.000141)	0.00021 (0.00101)	1e-05 (1e-04)	2e-05 (0.000141)
del 3p22 2	14 (11%)	109	6e-05 (0.000327)	1e-05 (1e-04)	0.00669 (0.0196)	1e-05 (1e-04)	0.0324 (0.0647)	0.0152 (0.0379)	0.0245 (0.0564)	0.0656 (0.104)	0.00055 (0.00236)	0.0296 (0.0635)
del 11q22 1	7 (6%)	116	9e-05 (0.00047)	2e-05 (0.000141)	0.0281 (0.0625)	0.00598 (0.0184)	0.0317 (0.0647)	0.0138 (0.0369)	0.0337 (0.0653)	0.114 (0.159)	0.00217 (0.00766)	0.00873 (0.0249)
del 9p21 3	11 (9%)	112	0.0158 (0.0379)	0.00366 (0.0125)	0.0795 (0.119)	0.00129 (0.00499)	5e-05 (0.000286)	1e-05 (1e-04)	0.558 (0.62)	0.00019 (0.00095)	0.143 (0.196)	0.0157 (0.0379)
del 9q22 33	3 (2%)	120	0.603 (0.658)	0.177 (0.23)	0.0421 (0.0778)	0.0145 (0.0379)	0.0495 (0.0861)	0.0294 (0.0635)	0.197 (0.25)	0.0667 (0.104)	0.106 (0.152)	0.0582 (0.0983)
del 19p13 11	5 (4%)	118	0.259 (0.308)	0.0441 (0.0798)	0.177 (0.23)	0.203 (0.251)	0.00202 (0.00735)	0.00035 (0.00156)	0.724 (0.755)	0.00487 (0.0155)	0.574 (0.632)	0.172 (0.229)
del 22q12 1	19 (15%)	104	1e-05 (1e-04)	0.0136 (0.0369)	0.0133 (0.0369)	0.0556 (0.0953)	0.0155 (0.0379)	0.0731 (0.112)	0.245 (0.294)	0.456 (0.516)	0.522 (0.585)	0.429 (0.49)
del 2q37 1	5 (4%)	118	0.262 (0.308)	0.0446 (0.0798)	0.0329 (0.0647)	0.112 (0.159)	0.629 (0.668)	0.307 (0.354)	1 (1.00)	0.0201 (0.0473)	1 (1.00)	0.169 (0.227)
del 7q36 3	3 (2%)	120	0.0597 (0.0995)	0.178 (0.23)	0.0421 (0.0778)	0.202 (0.251)	0.00115 (0.00476)	0.00391 (0.013)	0.648 (0.682)	0.117 (0.162)	0.106 (0.152)	0.617 (0.667)
del 10q26 3	6 (5%)	117	0.625 (0.668)	0.0388 (0.0739)	0.0917 (0.134)	0.0319 (0.0647)	0.0659 (0.104)	0.223 (0.27)	0.739 (0.765)	0.0666 (0.104)	0.856 (0.878)	0.0488 (0.0861)
del 22q13 32	15 (12%)	108	3e-05 (0.000189)	0.0852 (0.126)	0.0304 (0.064)	0.0793 (0.119)	0.0648 (0.104)	0.0249 (0.0564)	0.207 (0.254)	0.297 (0.347)	0.198 (0.25)	0.898 (0.914)

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.08

Table S1. Gene #1: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	36	24	24
DEL PEAK 1(2Q37.1) MUTATED	0	4	1	0
DEL PEAK 1(2Q37.1) WILD-TYPE	39	32	23	24

Figure S1. Get High-res Image Gene #1: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.1' versus 'RPPA_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.065

Table S2. Gene #1: 'del_2q37.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	39
DEL PEAK 1(2Q37.1) MUTATED	1	3	0
DEL PEAK 1(2Q37.1) WILD-TYPE	26	21	39

Figure S2. Get High-res Image Gene #1: 'del_2q37.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.047

Table S3. Gene #1: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	27	18	28	7	16	27
DEL PEAK 1(2Q37.1) MUTATED	0	3	1	1	0	0
DEL PEAK 1(2Q37.1) WILD-TYPE	27	15	27	6	16	27

Figure S3. Get High-res Image Gene #1: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00033

Table S4. Gene #2: 'del_3p22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	31	27
DEL PEAK 2(3P22.2) MUTATED	1	10	3
DEL PEAK 2(3P22.2) WILD-TYPE	64	21	24

Figure S4. Get High-res Image Gene #2: '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 = 1e-04

Table S5. Gene #2: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	36	24	24
DEL PEAK 2(3P22.2) MUTATED	0	3	10	1
DEL PEAK 2(3P22.2) WILD-TYPE	39	33	14	23

Figure S5. Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.2' versus 'RPPA_CNMF'

P value = 0.00669 (Fisher's exact test), Q value = 0.02

Table S6. Gene #2: 'del_3p22.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	39
DEL PEAK 2(3P22.2) MUTATED	8	1	2
DEL PEAK 2(3P22.2) WILD-TYPE	19	23	37

Figure S6. Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p22.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S7. Gene #2: 'del_3p22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	23	31	20
DEL PEAK 2(3P22.2) MUTATED	3	0	0	8
DEL PEAK 2(3P22.2) WILD-TYPE	13	23	31	12

Figure S7. Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.065

Table S8. Gene #2: 'del_3p22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	31	29	14
DEL PEAK 2(3P22.2) MUTATED	9	1	1	3
DEL PEAK 2(3P22.2) WILD-TYPE	36	30	28	11

Figure S8. Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.038

Table S9. Gene #2: 'del_3p22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	42	20	10
DEL PEAK 2(3P22.2) MUTATED	10	1	1	2
DEL PEAK 2(3P22.2) WILD-TYPE	37	41	19	8

Figure S9. Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.056

Table S10. Gene #2: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	61	1	2	1
DEL PEAK 2(3P22.2) MUTATED	12	2	0	0	0
DEL PEAK 2(3P22.2) WILD-TYPE	46	59	1	2	1

Figure S10. Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0024

Table S11. Gene #2: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	59	46
DEL PEAK 2(3P22.2) MUTATED	0	2	12
DEL PEAK 2(3P22.2) WILD-TYPE	18	57	34

Figure S11. Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.064

Table S12. Gene #2: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	33	33	28
DEL PEAK 2(3P22.2) MUTATED	7	1	5	1
DEL PEAK 2(3P22.2) WILD-TYPE	22	32	28	27

Figure S12. Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S13. Gene #3: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	31	27
DEL PEAK 3(6P25.2) MUTATED	1	20	5
DEL PEAK 3(6P25.2) WILD-TYPE	64	11	22

Figure S13. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S14. Gene #3: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	36	24	24
DEL PEAK 3(6P25.2) MUTATED	2	6	15	3
DEL PEAK 3(6P25.2) WILD-TYPE	37	30	9	21

Figure S14. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.2' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S15. Gene #3: 'del_6p25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	39
DEL PEAK 3(6P25.2) MUTATED	15	4	2
DEL PEAK 3(6P25.2) WILD-TYPE	12	20	37

Figure S15. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p25.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S16. Gene #3: 'del_6p25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	23	31	20
DEL PEAK 3(6P25.2) MUTATED	3	4	2	12
DEL PEAK 3(6P25.2) WILD-TYPE	13	19	29	8

Figure S16. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6p25.2' versus 'MRNASEQ_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0065

Table S17. Gene #3: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	31	29	14
DEL PEAK 3(6P25.2) MUTATED	14	1	4	6
DEL PEAK 3(6P25.2) WILD-TYPE	31	30	25	8

Figure S17. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S18. Gene #3: 'del_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	42	20	10
DEL PEAK 3(6P25.2) MUTATED	15	4	0	6
DEL PEAK 3(6P25.2) WILD-TYPE	32	38	20	4

Figure S18. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0048

Table S19. Gene #3: 'del_6p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	61	1	2	1
DEL PEAK 3(6P25.2) MUTATED	20	5	0	1	0
DEL PEAK 3(6P25.2) WILD-TYPE	38	56	1	1	1

Figure S19. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00654 (Fisher's exact test), Q value = 0.02

Table S20. Gene #3: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	27	18	28	7	16	27
DEL PEAK 3(6P25.2) MUTATED	10	3	8	3	0	2
DEL PEAK 3(6P25.2) WILD-TYPE	17	15	20	4	16	25

Figure S20. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S21. Gene #3: 'del_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	59	46
DEL PEAK 3(6P25.2) MUTATED	1	5	20
DEL PEAK 3(6P25.2) WILD-TYPE	17	54	26

Figure S21. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.016

Table S22. Gene #3: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	33	33	28
DEL PEAK 3(6P25.2) MUTATED	11	3	10	2
DEL PEAK 3(6P25.2) WILD-TYPE	18	30	23	26

Figure S22. Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S23. Gene #4: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	31	27
DEL PEAK 4(6Q21) MUTATED	0	18	2
DEL PEAK 4(6Q21) WILD-TYPE	65	13	25

Figure S23. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S24. Gene #4: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	36	24	24
DEL PEAK 4(6Q21) MUTATED	1	3	16	0
DEL PEAK 4(6Q21) WILD-TYPE	38	33	8	24

Figure S24. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S25. Gene #4: 'del_6q21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	39
DEL PEAK 4(6Q21) MUTATED	13	1	1
DEL PEAK 4(6Q21) WILD-TYPE	14	23	38

Figure S25. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q21' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S26. Gene #4: 'del_6q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	23	31	20
DEL PEAK 4(6Q21) MUTATED	2	1	1	11
DEL PEAK 4(6Q21) WILD-TYPE	14	22	30	9

Figure S26. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S27. Gene #4: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	31	29	14
DEL PEAK 4(6Q21) MUTATED	13	0	0	7
DEL PEAK 4(6Q21) WILD-TYPE	32	31	29	7

Figure S27. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S28. Gene #4: 'del_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	42	20	10
DEL PEAK 4(6Q21) MUTATED	14	0	1	5
DEL PEAK 4(6Q21) WILD-TYPE	33	42	19	5

Figure S28. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q21' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S29. Gene #4: 'del_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	61	1	2	1
DEL PEAK 4(6Q21) MUTATED	18	1	0	1	0
DEL PEAK 4(6Q21) WILD-TYPE	40	60	1	1	1

Figure S29. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.001

Table S30. Gene #4: 'del_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	27	18	28	7	16	27
DEL PEAK 4(6Q21) MUTATED	9	0	7	3	1	0
DEL PEAK 4(6Q21) WILD-TYPE	18	18	21	4	15	27

Figure S30. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S31. Gene #4: 'del_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	59	46
DEL PEAK 4(6Q21) MUTATED	0	0	20
DEL PEAK 4(6Q21) WILD-TYPE	18	59	26

Figure S31. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S32. Gene #4: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	33	33	28
DEL PEAK 4(6Q21) MUTATED	10	1	9	0
DEL PEAK 4(6Q21) WILD-TYPE	19	32	24	28

Figure S32. Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'RPPA_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.078

Table S33. Gene #5: 'del_7q36.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	39
DEL PEAK 5(7Q36.3) MUTATED	3	0	0
DEL PEAK 5(7Q36.3) WILD-TYPE	24	24	39

Figure S33. Get High-res Image Gene #5: 'del_7q36.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0048

Table S34. Gene #5: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	31	29	14
DEL PEAK 5(7Q36.3) MUTATED	0	0	0	3
DEL PEAK 5(7Q36.3) WILD-TYPE	45	31	29	11

Figure S34. Get High-res Image Gene #5: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00391 (Fisher's exact test), Q value = 0.013

Table S35. Gene #5: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	42	20	10
DEL PEAK 5(7Q36.3) MUTATED	0	0	1	2
DEL PEAK 5(7Q36.3) WILD-TYPE	47	42	19	8

Figure S35. Get High-res Image Gene #5: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.038

Table S36. Gene #6: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	31	27
DEL PEAK 6(9P21.3) MUTATED	2	6	3
DEL PEAK 6(9P21.3) WILD-TYPE	63	25	24

Figure S36. Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.013

Table S37. Gene #6: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	36	24	24
DEL PEAK 6(9P21.3) MUTATED	0	8	2	1
DEL PEAK 6(9P21.3) WILD-TYPE	39	28	22	23

Figure S37. Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.005

Table S38. Gene #6: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	23	31	20
DEL PEAK 6(9P21.3) MUTATED	0	3	0	6
DEL PEAK 6(9P21.3) WILD-TYPE	16	20	31	14

Figure S38. Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00029

Table S39. Gene #6: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	31	29	14
DEL PEAK 6(9P21.3) MUTATED	1	0	3	6
DEL PEAK 6(9P21.3) WILD-TYPE	44	31	26	8

Figure S39. Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S40. Gene #6: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	42	20	10
DEL PEAK 6(9P21.3) MUTATED	1	0	3	6
DEL PEAK 6(9P21.3) WILD-TYPE	46	42	17	4

Figure S40. Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00095

Table S41. Gene #6: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	27	18	28	7	16	27
DEL PEAK 6(9P21.3) MUTATED	0	0	3	4	3	1
DEL PEAK 6(9P21.3) WILD-TYPE	27	18	25	3	13	26

Figure S41. Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.038

Table S42. Gene #6: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	33	33	28
DEL PEAK 6(9P21.3) MUTATED	0	3	7	1
DEL PEAK 6(9P21.3) WILD-TYPE	29	30	26	27

Figure S42. Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q22.33' versus 'RPPA_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.078

Table S43. Gene #7: 'del_9q22.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	39
DEL PEAK 7(9Q22.33) MUTATED	3	0	0
DEL PEAK 7(9Q22.33) WILD-TYPE	24	24	39

Figure S43. Get High-res Image Gene #7: 'del_9q22.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9q22.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.038

Table S44. Gene #7: 'del_9q22.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	23	31	20
DEL PEAK 7(9Q22.33) MUTATED	0	0	0	3
DEL PEAK 7(9Q22.33) WILD-TYPE	16	23	31	17

Figure S44. Get High-res Image Gene #7: 'del_9q22.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9q22.33' versus 'MRNASEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.086

Table S45. Gene #7: 'del_9q22.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	31	29	14
DEL PEAK 7(9Q22.33) MUTATED	1	0	0	2
DEL PEAK 7(9Q22.33) WILD-TYPE	44	31	29	12

Figure S45. Get High-res Image Gene #7: 'del_9q22.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.064

Table S46. Gene #7: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	42	20	10
DEL PEAK 7(9Q22.33) MUTATED	1	0	0	2
DEL PEAK 7(9Q22.33) WILD-TYPE	46	42	20	8

Figure S46. Get High-res Image Gene #7: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.074

Table S47. Gene #8: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	36	24	24
DEL PEAK 8(10Q26.3) MUTATED	0	3	3	0
DEL PEAK 8(10Q26.3) WILD-TYPE	39	33	21	24

Figure S47. Get High-res Image Gene #8: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.065

Table S48. Gene #8: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	23	31	20
DEL PEAK 8(10Q26.3) MUTATED	0	4	0	1
DEL PEAK 8(10Q26.3) WILD-TYPE	16	19	31	19

Figure S48. Get High-res Image Gene #8: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 0.086

Table S49. Gene #8: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	33	33	28
DEL PEAK 8(10Q26.3) MUTATED	2	4	0	0
DEL PEAK 8(10Q26.3) WILD-TYPE	27	29	33	28

Figure S49. Get High-res Image Gene #8: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00047

Table S50. Gene #9: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	31	27
DEL PEAK 9(11Q22.1) MUTATED	0	7	0
DEL PEAK 9(11Q22.1) WILD-TYPE	65	24	27

Figure S50. Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S51. Gene #9: 'del_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	36	24	24
DEL PEAK 9(11Q22.1) MUTATED	0	0	7	0
DEL PEAK 9(11Q22.1) WILD-TYPE	39	36	17	24

Figure S51. Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q22.1' versus 'RPPA_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.062

Table S52. Gene #9: 'del_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	39
DEL PEAK 9(11Q22.1) MUTATED	4	1	0
DEL PEAK 9(11Q22.1) WILD-TYPE	23	23	39

Figure S52. Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00598 (Fisher's exact test), Q value = 0.018

Table S53. Gene #9: 'del_11q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	23	31	20
DEL PEAK 9(11Q22.1) MUTATED	1	0	0	4
DEL PEAK 9(11Q22.1) WILD-TYPE	15	23	31	16

Figure S53. Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.065

Table S54. Gene #9: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	31	29	14
DEL PEAK 9(11Q22.1) MUTATED	6	0	0	1
DEL PEAK 9(11Q22.1) WILD-TYPE	39	31	29	13

Figure S54. Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.037

Table S55. Gene #9: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	42	20	10
DEL PEAK 9(11Q22.1) MUTATED	7	0	0	0
DEL PEAK 9(11Q22.1) WILD-TYPE	40	42	20	10

Figure S55. Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.065

Table S56. Gene #9: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	58	61	1	2	1
DEL PEAK 9(11Q22.1) MUTATED	7	0	0	0	0
DEL PEAK 9(11Q22.1) WILD-TYPE	51	61	1	2	1

Figure S56. Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0077

Table S57. Gene #9: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	59	46
DEL PEAK 9(11Q22.1) MUTATED	0	0	7
DEL PEAK 9(11Q22.1) WILD-TYPE	18	59	39

Figure S57. Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00873 (Fisher's exact test), Q value = 0.025

Table S58. Gene #9: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	33	33	28
DEL PEAK 9(11Q22.1) MUTATED	5	0	2	0
DEL PEAK 9(11Q22.1) WILD-TYPE	24	33	31	28

Figure S58. Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.11' versus 'METHLYATION_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.08

Table S59. Gene #10: 'del_19p13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	36	24	24
DEL PEAK 10(19P13.11) MUTATED	0	4	1	0
DEL PEAK 10(19P13.11) WILD-TYPE	39	32	23	24

Figure S59. Get High-res Image Gene #10: 'del_19p13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.11' versus 'MRNASEQ_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0073

Table S60. Gene #10: 'del_19p13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	31	29	14
DEL PEAK 10(19P13.11) MUTATED	0	0	2	3
DEL PEAK 10(19P13.11) WILD-TYPE	45	31	27	11

Figure S60. Get High-res Image Gene #10: 'del_19p13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0016

Table S61. Gene #10: 'del_19p13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	42	20	10
DEL PEAK 10(19P13.11) MUTATED	0	0	2	3
DEL PEAK 10(19P13.11) WILD-TYPE	47	42	18	7

Figure S61. Get High-res Image Gene #10: 'del_19p13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00487 (Fisher's exact test), Q value = 0.016

Table S62. Gene #10: 'del_19p13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	27	18	28	7	16	27
DEL PEAK 10(19P13.11) MUTATED	0	0	1	2	2	0
DEL PEAK 10(19P13.11) WILD-TYPE	27	18	27	5	14	27

Figure S62. Get High-res Image Gene #10: 'del_19p13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S63. Gene #11: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	31	27
DEL PEAK 11(22Q12.1) MUTATED	0	4	15
DEL PEAK 11(22Q12.1) WILD-TYPE	65	27	12

Figure S63. Get High-res Image Gene #11: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.1' versus 'METHLYATION_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.037

Table S64. Gene #11: 'del_22q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	36	24	24
DEL PEAK 11(22Q12.1) MUTATED	1	9	3	6
DEL PEAK 11(22Q12.1) WILD-TYPE	38	27	21	18

Figure S64. Get High-res Image Gene #11: 'del_22q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.1' versus 'RPPA_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.037

Table S65. Gene #11: 'del_22q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	39
DEL PEAK 11(22Q12.1) MUTATED	4	8	2
DEL PEAK 11(22Q12.1) WILD-TYPE	23	16	37

Figure S65. Get High-res Image Gene #11: 'del_22q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.038

Table S66. Gene #11: 'del_22q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	31	29	14
DEL PEAK 11(22Q12.1) MUTATED	2	5	8	4
DEL PEAK 11(22Q12.1) WILD-TYPE	43	26	21	10

Figure S66. Get High-res Image Gene #11: 'del_22q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S67. Gene #12: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	31	27
DEL PEAK 12(22Q13.32) MUTATED	1	4	10
DEL PEAK 12(22Q13.32) WILD-TYPE	64	27	17

Figure S67. Get High-res Image Gene #12: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.064

Table S68. Gene #12: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	39
DEL PEAK 12(22Q13.32) MUTATED	5	5	1
DEL PEAK 12(22Q13.32) WILD-TYPE	22	19	38

Figure S68. Get High-res Image Gene #12: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.056

Table S69. Gene #12: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	42	20	10
DEL PEAK 12(22Q13.32) MUTATED	3	4	4	4
DEL PEAK 12(22Q13.32) WILD-TYPE	44	38	16	6

Figure S69. Get High-res Image Gene #12: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_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/THYM-TP/15104465/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/15111344/THYM-TP.transferedmergedcluster.txt
Number of patients = 123
Number of significantly focal cnvs = 12
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

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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