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

Pheochromocytoma and Paraganglioma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1MW2GM7

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 28 focal events and 10 molecular subtypes across 162 patients, 93 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_4q31.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.
amp_11p15.2 cnv correlated to 'CN_CNMF'.
amp_12q13.3 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.
amp_17q21.31 cnv correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.2 cnv correlated to 'CN_CNMF'.
del_6p12.3 cnv correlated to 'MRNASEQ_CNMF'.
del_6q16.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p22 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_8q23.3 cnv correlated to 'MIRSEQ_CNMF'.
del_9q21.12 cnv correlated to 'RPPA_CNMF'.
del_11p15.4 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q22.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q21 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_17p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', '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 28 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, 93 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 1p12	113 (70%)	49	1e-05 (0.000215)	1e-05 (0.000215)	0.305 (0.466)	0.00137 (0.00984)	1e-05 (0.000215)	3e-05 (0.000467)	0.0016 (0.0112)	0.0167 (0.0678)	0.0159 (0.0668)	0.00125 (0.00921)
del 3q26 1	93 (57%)	69	1e-05 (0.000215)	0.643 (0.757)	0.0162 (0.0668)	0.0145 (0.0644)	0.0283 (0.101)	1e-05 (0.000215)	0.00253 (0.0168)	0.0092 (0.0452)	0.00193 (0.0132)	0.00011 (0.0014)
del 3p24 1	64 (40%)	98	0.00845 (0.043)	0.0422 (0.136)	0.225 (0.396)	0.0859 (0.202)	3e-05 (0.000467)	2e-05 (0.00035)	2e-05 (0.00035)	0.00024 (0.0028)	1e-05 (0.000215)	1e-05 (0.000215)
del 11p15 4	58 (36%)	104	0.0148 (0.0644)	4e-05 (0.00056)	0.0943 (0.218)	0.113 (0.25)	0.0008 (0.00659)	1e-05 (0.000215)	6e-05 (8e-04)	1e-05 (0.000215)	1e-05 (0.000215)	1e-05 (0.000215)
del xp21 1	46 (28%)	116	0.0003 (0.00321)	0.00074 (0.00659)	0.0469 (0.143)	0.243 (0.418)	0.036 (0.121)	0.00358 (0.0228)	0.00027 (0.00302)	0.0462 (0.143)	0.311 (0.474)	0.0184 (0.0735)
del 6q16 1	24 (15%)	138	0.0446 (0.142)	0.066 (0.172)	0.04 (0.13)	0.217 (0.39)	0.0313 (0.108)	0.00769 (0.0421)	0.016 (0.0668)	0.00587 (0.0357)	0.0573 (0.162)	0.0206 (0.0789)
del 11q22 1	50 (31%)	112	2e-05 (0.00035)	0.139 (0.289)	0.182 (0.342)	0.0608 (0.162)	0.0002 (0.00243)	0.00465 (0.0289)	0.00094 (0.00731)	0.00079 (0.00659)	0.0006 (0.0056)	4e-05 (0.00056)
del 17p13 2	64 (40%)	98	0.00031 (0.00321)	0.00097 (0.00734)	0.409 (0.566)	0.0664 (0.172)	0.00884 (0.0442)	0.00627 (0.0366)	0.0203 (0.0789)	0.00821 (0.043)	0.169 (0.329)	0.0295 (0.103)
del 22q13 31	65 (40%)	97	1e-05 (0.000215)	0.0107 (0.0509)	0.729 (0.814)	0.0583 (0.162)	0.0107 (0.0509)	0.00052 (0.0052)	0.0067 (0.0383)	0.0272 (0.1)	0.047 (0.143)	0.0654 (0.172)
del 17q11 2	42 (26%)	120	0.0008 (0.00659)	0.00622 (0.0366)	0.0245 (0.0923)	0.131 (0.279)	0.0329 (0.112)	0.00258 (0.0168)	0.103 (0.235)	0.0705 (0.176)	0.188 (0.348)	0.00782 (0.0421)
amp 17q21 31	16 (10%)	146	0.0674 (0.172)	1 (1.00)	0.407 (0.566)	0.353 (0.512)	0.518 (0.671)	0.00056 (0.00541)	0.948 (0.983)	0.143 (0.295)	0.0123 (0.0566)	0.0131 (0.059)
amp 1q21 3	30 (19%)	132	1e-05 (0.000215)	0.0389 (0.128)	0.91 (0.956)	0.799 (0.874)	0.72 (0.806)	0.941 (0.98)	0.714 (0.805)	0.445 (0.608)	0.0587 (0.162)	0.211 (0.381)
amp 4q31 1	15 (9%)	147	0.0594 (0.162)	0.227 (0.397)	0.619 (0.738)	0.0503 (0.15)	0.29 (0.46)	0.00088 (0.00704)	0.62 (0.738)	0.256 (0.434)	0.0118 (0.0553)	0.0691 (0.174)
amp 12q13 3	16 (10%)	146	0.126 (0.27)	0.135 (0.284)	0.756 (0.837)	0.322 (0.483)	0.827 (0.894)	0.622 (0.738)	0.0286 (0.101)	0.275 (0.45)	0.015 (0.0644)	0.108 (0.241)
del 8p22	25 (15%)	137	0.0526 (0.155)	0.206 (0.375)	0.57 (0.716)	0.646 (0.757)	0.0078 (0.0421)	0.00841 (0.043)	0.121 (0.264)	0.24 (0.418)	0.175 (0.334)	0.293 (0.46)
amp 11p15 2	8 (5%)	154	0.0467 (0.143)	0.06 (0.162)	0.344 (0.504)	0.224 (0.396)	0.329 (0.487)	0.101 (0.232)	0.305 (0.466)	0.395 (0.559)	0.0676 (0.172)	0.139 (0.289)
del 4q34 2	13 (8%)	149	0.0478 (0.144)	0.293 (0.46)	0.516 (0.671)	0.316 (0.478)	0.055 (0.159)	0.493 (0.654)	0.509 (0.669)	0.899 (0.95)	0.295 (0.46)	0.346 (0.504)
del 6p12 3	10 (6%)	152	0.505 (0.666)	0.269 (0.446)			0.02 (0.0789)	0.0869 (0.203)	0.29 (0.46)	0.164 (0.324)	0.668 (0.776)	0.2 (0.368)
del 8q23 3	13 (8%)	149	0.0853 (0.202)	1 (1.00)	0.481 (0.648)	1 (1.00)	0.265 (0.444)	0.522 (0.671)	0.0372 (0.124)	0.465 (0.629)	0.753 (0.836)	0.328 (0.487)
del 9q21 12	14 (9%)	148	0.519 (0.671)	0.157 (0.316)	0.0247 (0.0923)	0.0601 (0.162)	0.397 (0.559)	0.391 (0.559)	0.529 (0.673)	0.113 (0.25)	0.432 (0.593)	0.395 (0.559)
del 16q21	5 (3%)	157	0.528 (0.673)	0.716 (0.805)	0.696 (0.801)	0.788 (0.866)	0.547 (0.693)	0.0276 (0.1)	0.261 (0.441)	0.591 (0.729)	0.333 (0.491)	0.645 (0.757)
amp 14q24 3	10 (6%)	152	0.28 (0.453)	0.582 (0.725)	0.71 (0.805)	0.162 (0.324)	1 (1.00)	0.175 (0.334)	0.458 (0.623)	0.714 (0.805)	0.271 (0.447)	0.933 (0.975)
del 1q44	21 (13%)	141	0.587 (0.728)	0.57 (0.716)	0.0832 (0.199)	0.153 (0.312)	0.219 (0.39)	0.277 (0.451)	0.406 (0.566)	0.705 (0.805)	0.173 (0.334)	0.652 (0.761)
del 4q22 1	13 (8%)	149	0.296 (0.46)	0.611 (0.737)	0.202 (0.37)	0.597 (0.732)	0.0543 (0.158)	0.269 (0.446)	0.355 (0.513)	0.492 (0.654)	0.492 (0.654)	0.169 (0.329)
del 5q15	12 (7%)	150	0.076 (0.187)	0.683 (0.79)	0.0602 (0.162)	0.804 (0.876)	1 (1.00)	1 (1.00)	0.869 (0.932)	0.186 (0.347)	0.286 (0.46)	0.243 (0.418)
del 9p24 2	15 (9%)	147	0.132 (0.279)	0.0746 (0.185)	0.083 (0.199)	0.163 (0.324)	0.107 (0.241)	0.177 (0.334)	0.521 (0.671)	0.0779 (0.19)	0.154 (0.312)	0.125 (0.27)
del 12q21 33	8 (5%)	154	0.255 (0.434)	0.582 (0.725)	0.616 (0.738)	0.606 (0.737)	0.912 (0.956)	0.876 (0.937)	0.598 (0.732)	0.698 (0.801)	0.844 (0.909)	0.884 (0.941)
del 13q22 3	8 (5%)	154	1 (1.00)	0.812 (0.881)	0.323 (0.483)	0.788 (0.866)	0.297 (0.46)	0.429 (0.592)	1 (1.00)	0.61 (0.737)	0.395 (0.559)	0.9 (0.95)

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S1. Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
AMP PEAK 1(1Q21.3) MUTATED	17	0	0	11	2
AMP PEAK 1(1Q21.3) WILD-TYPE	20	40	10	39	23

Figure S1. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.13

Table S2. Gene #1: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	45
AMP PEAK 1(1Q21.3) MUTATED	10	17	3
AMP PEAK 1(1Q21.3) WILD-TYPE	30	60	42

Figure S2. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.007

Table S3. Gene #2: 'amp_4q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
AMP PEAK 2(4Q31.1) MUTATED	9	5	0	1
AMP PEAK 2(4Q31.1) WILD-TYPE	25	59	43	20

Figure S3. Get High-res Image Gene #2: 'amp_4q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.055

Table S4. Gene #2: 'amp_4q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	50	16	33	29
AMP PEAK 2(4Q31.1) MUTATED	6	4	4	1	0
AMP PEAK 2(4Q31.1) WILD-TYPE	27	46	12	32	29

Figure S4. Get High-res Image Gene #2: 'amp_4q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11p15.2' versus 'CN_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.14

Table S5. Gene #3: 'amp_11p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
AMP PEAK 3(11P15.2) MUTATED	3	0	2	3	0
AMP PEAK 3(11P15.2) WILD-TYPE	34	40	8	47	25

Figure S5. Get High-res Image Gene #3: 'amp_11p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.1

Table S6. Gene #4: 'amp_12q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
AMP PEAK 4(12Q13.3) MUTATED	11	1	4
AMP PEAK 4(12Q13.3) WILD-TYPE	52	43	51

Figure S6. Get High-res Image Gene #4: 'amp_12q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.064

Table S7. Gene #4: 'amp_12q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	50	16	33	29
AMP PEAK 4(12Q13.3) MUTATED	3	5	0	8	0
AMP PEAK 4(12Q13.3) WILD-TYPE	30	45	16	25	29

Figure S7. Get High-res Image Gene #4: 'amp_12q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0054

Table S8. Gene #6: 'amp_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
AMP PEAK 6(17Q21.31) MUTATED	10	5	1	0
AMP PEAK 6(17Q21.31) WILD-TYPE	24	59	42	21

Figure S8. Get High-res Image Gene #6: 'amp_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.057

Table S9. Gene #6: 'amp_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	50	16	33	29
AMP PEAK 6(17Q21.31) MUTATED	6	5	4	0	1
AMP PEAK 6(17Q21.31) WILD-TYPE	27	45	12	33	28

Figure S9. Get High-res Image Gene #6: 'amp_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.059

Table S10. Gene #6: 'amp_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
AMP PEAK 6(17Q21.31) MUTATED	2	3	8	1	0	2	0
AMP PEAK 6(17Q21.31) WILD-TYPE	16	38	19	14	23	16	19

Figure S10. Get High-res Image Gene #6: 'amp_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S11. Gene #7: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 1(1P12) MUTATED	28	14	8	40	23
DEL PEAK 1(1P12) WILD-TYPE	9	26	2	10	2

Figure S11. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S12. Gene #7: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	45
DEL PEAK 1(1P12) MUTATED	25	67	21
DEL PEAK 1(1P12) WILD-TYPE	15	10	24

Figure S12. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0098

Table S13. Gene #7: 'del_1p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	18	28
DEL PEAK 1(1P12) MUTATED	15	17	22
DEL PEAK 1(1P12) WILD-TYPE	16	1	6

Figure S13. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S14. Gene #7: 'del_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 1(1P12) MUTATED	23	59	21	10
DEL PEAK 1(1P12) WILD-TYPE	9	6	23	11

Figure S14. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00047

Table S15. Gene #7: 'del_1p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 1(1P12) MUTATED	19	58	27	9
DEL PEAK 1(1P12) WILD-TYPE	15	6	16	12

Figure S15. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p12' versus 'MIRSEQ_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.011

Table S16. Gene #7: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 1(1P12) MUTATED	38	27	48
DEL PEAK 1(1P12) WILD-TYPE	25	17	7

Figure S16. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.068

Table S17. Gene #7: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	54	18	24
DEL PEAK 1(1P12) MUTATED	41	46	12	14
DEL PEAK 1(1P12) WILD-TYPE	25	8	6	10

Figure S17. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.067

Table S18. Gene #7: 'del_1p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	50	16	33	29
DEL PEAK 1(1P12) MUTATED	20	43	13	20	17
DEL PEAK 1(1P12) WILD-TYPE	13	7	3	13	12

Figure S18. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.0092

Table S19. Gene #7: 'del_1p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
DEL PEAK 1(1P12) MUTATED	11	35	19	15	12	12	9
DEL PEAK 1(1P12) WILD-TYPE	7	6	8	0	11	6	10

Figure S19. Get High-res Image Gene #7: 'del_1p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p24.1' versus 'CN_CNMF'

P value = 0.00845 (Fisher's exact test), Q value = 0.043

Table S20. Gene #9: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 3(3P24.1) MUTATED	13	15	1	29	6
DEL PEAK 3(3P24.1) WILD-TYPE	24	25	9	21	19

Figure S20. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'METHLYATION_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.14

Table S21. Gene #9: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	45
DEL PEAK 3(3P24.1) MUTATED	21	23	20
DEL PEAK 3(3P24.1) WILD-TYPE	19	54	25

Figure S21. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00047

Table S22. Gene #9: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 3(3P24.1) MUTATED	18	15	27	4
DEL PEAK 3(3P24.1) WILD-TYPE	14	50	17	17

Figure S22. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S23. Gene #9: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 3(3P24.1) MUTATED	12	17	31	4
DEL PEAK 3(3P24.1) WILD-TYPE	22	47	12	17

Figure S23. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S24. Gene #9: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 3(3P24.1) MUTATED	38	7	19
DEL PEAK 3(3P24.1) WILD-TYPE	25	37	36

Figure S24. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0028

Table S25. Gene #9: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	54	18	24
DEL PEAK 3(3P24.1) MUTATED	39	15	6	4
DEL PEAK 3(3P24.1) WILD-TYPE	27	39	12	20

Figure S25. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S26. Gene #9: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	50	16	33	29
DEL PEAK 3(3P24.1) MUTATED	11	15	3	27	8
DEL PEAK 3(3P24.1) WILD-TYPE	22	35	13	6	21

Figure S26. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S27. Gene #9: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
DEL PEAK 3(3P24.1) MUTATED	6	15	13	1	20	6	3
DEL PEAK 3(3P24.1) WILD-TYPE	12	26	14	14	3	12	16

Figure S27. Get High-res Image Gene #9: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S28. Gene #10: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 4(3Q26.1) MUTATED	9	12	6	45	21
DEL PEAK 4(3Q26.1) WILD-TYPE	28	28	4	5	4

Figure S28. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.1' versus 'RPPA_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.067

Table S29. Gene #10: 'del_3q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	20	23	18
DEL PEAK 4(3Q26.1) MUTATED	10	15	16	5
DEL PEAK 4(3Q26.1) WILD-TYPE	6	5	7	13

Figure S29. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3q26.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.064

Table S30. Gene #10: 'del_3q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	18	28
DEL PEAK 4(3Q26.1) MUTATED	13	15	18
DEL PEAK 4(3Q26.1) WILD-TYPE	18	3	10

Figure S30. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3q26.1' versus 'MRNASEQ_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.1

Table S31. Gene #10: 'del_3q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 4(3Q26.1) MUTATED	20	44	22	7
DEL PEAK 4(3Q26.1) WILD-TYPE	12	21	22	14

Figure S31. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S32. Gene #10: 'del_3q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 4(3Q26.1) MUTATED	6	47	33	7
DEL PEAK 4(3Q26.1) WILD-TYPE	28	17	10	14

Figure S32. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.1' versus 'MIRSEQ_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.017

Table S33. Gene #10: 'del_3q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 4(3Q26.1) MUTATED	38	16	39
DEL PEAK 4(3Q26.1) WILD-TYPE	25	28	16

Figure S33. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0092 (Fisher's exact test), Q value = 0.045

Table S34. Gene #10: 'del_3q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	54	18	24
DEL PEAK 4(3Q26.1) MUTATED	39	38	5	11
DEL PEAK 4(3Q26.1) WILD-TYPE	27	16	13	13

Figure S34. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.013

Table S35. Gene #10: 'del_3q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	50	16	33	29
DEL PEAK 4(3Q26.1) MUTATED	10	36	8	23	16
DEL PEAK 4(3Q26.1) WILD-TYPE	23	14	8	10	13

Figure S35. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0014

Table S36. Gene #10: 'del_3q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
DEL PEAK 4(3Q26.1) MUTATED	5	31	16	9	19	5	8
DEL PEAK 4(3Q26.1) WILD-TYPE	13	10	11	6	4	13	11

Figure S36. Get High-res Image Gene #10: 'del_3q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.2' versus 'CN_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.14

Table S37. Gene #12: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 6(4Q34.2) MUTATED	0	7	1	4	1
DEL PEAK 6(4Q34.2) WILD-TYPE	37	33	9	46	24

Figure S37. Get High-res Image Gene #12: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p12.3' versus 'MRNASEQ_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.079

Table S38. Gene #14: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 8(6P12.3) MUTATED	1	1	4	4
DEL PEAK 8(6P12.3) WILD-TYPE	31	64	40	17

Figure S38. Get High-res Image Gene #14: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q16.1' versus 'CN_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.14

Table S39. Gene #15: 'del_6q16.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 9(6Q16.1) MUTATED	3	3	4	11	3
DEL PEAK 9(6Q16.1) WILD-TYPE	34	37	6	39	22

Figure S39. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q16.1' versus 'RPPA_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.13

Table S40. Gene #15: 'del_6q16.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	20	23	18
DEL PEAK 9(6Q16.1) MUTATED	2	2	7	0
DEL PEAK 9(6Q16.1) WILD-TYPE	14	18	16	18

Figure S40. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q16.1' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.11

Table S41. Gene #15: 'del_6q16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 9(6Q16.1) MUTATED	1	15	4	4
DEL PEAK 9(6Q16.1) WILD-TYPE	31	50	40	17

Figure S41. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00769 (Fisher's exact test), Q value = 0.042

Table S42. Gene #15: 'del_6q16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 9(6Q16.1) MUTATED	1	16	3	4
DEL PEAK 9(6Q16.1) WILD-TYPE	33	48	40	17

Figure S42. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q16.1' versus 'MIRSEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.067

Table S43. Gene #15: 'del_6q16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 9(6Q16.1) MUTATED	4	6	14
DEL PEAK 9(6Q16.1) WILD-TYPE	59	38	41

Figure S43. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q16.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00587 (Fisher's exact test), Q value = 0.036

Table S44. Gene #15: 'del_6q16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	54	18	24
DEL PEAK 9(6Q16.1) MUTATED	4	15	1	4
DEL PEAK 9(6Q16.1) WILD-TYPE	62	39	17	20

Figure S44. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q16.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.079

Table S45. Gene #15: 'del_6q16.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
DEL PEAK 9(6Q16.1) MUTATED	0	11	1	4	3	1	4
DEL PEAK 9(6Q16.1) WILD-TYPE	18	30	26	11	20	17	15

Figure S45. Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 0.0078 (Fisher's exact test), Q value = 0.042

Table S46. Gene #16: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 10(8P22) MUTATED	3	18	3	1
DEL PEAK 10(8P22) WILD-TYPE	29	47	41	20

Figure S46. Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00841 (Fisher's exact test), Q value = 0.043

Table S47. Gene #16: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 10(8P22) MUTATED	5	17	2	1
DEL PEAK 10(8P22) WILD-TYPE	29	47	41	20

Figure S47. Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8q23.3' versus 'MIRSEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.12

Table S48. Gene #17: 'del_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 11(8Q23.3) MUTATED	6	0	7
DEL PEAK 11(8Q23.3) WILD-TYPE	57	44	48

Figure S48. Get High-res Image Gene #17: 'del_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q21.12' versus 'RPPA_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.092

Table S49. Gene #19: 'del_9q21.12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	20	23	18
DEL PEAK 13(9Q21.12) MUTATED	0	0	5	1
DEL PEAK 13(9Q21.12) WILD-TYPE	16	20	18	17

Figure S49. Get High-res Image Gene #19: 'del_9q21.12' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.4' versus 'CN_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.064

Table S50. Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 14(11P15.4) MUTATED	10	21	0	18	9
DEL PEAK 14(11P15.4) WILD-TYPE	27	19	10	32	16

Figure S50. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00056

Table S51. Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	45
DEL PEAK 14(11P15.4) MUTATED	22	14	22
DEL PEAK 14(11P15.4) WILD-TYPE	18	63	23

Figure S51. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0066

Table S52. Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 14(11P15.4) MUTATED	12	14	26	6
DEL PEAK 14(11P15.4) WILD-TYPE	20	51	18	15

Figure S52. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S53. Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 14(11P15.4) MUTATED	11	10	31	6
DEL PEAK 14(11P15.4) WILD-TYPE	23	54	12	15

Figure S53. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8e-04

Table S54. Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 14(11P15.4) MUTATED	36	10	12
DEL PEAK 14(11P15.4) WILD-TYPE	27	34	43

Figure S54. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S55. Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	54	18	24
DEL PEAK 14(11P15.4) MUTATED	39	8	5	6
DEL PEAK 14(11P15.4) WILD-TYPE	27	46	13	18

Figure S55. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S56. Gene #20: 'del_11p15.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	50	16	33	29
DEL PEAK 14(11P15.4) MUTATED	10	8	3	23	13
DEL PEAK 14(11P15.4) WILD-TYPE	23	42	13	10	16

Figure S56. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S57. Gene #20: 'del_11p15.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
DEL PEAK 14(11P15.4) MUTATED	9	7	8	2	21	5	5
DEL PEAK 14(11P15.4) WILD-TYPE	9	34	19	13	2	13	14

Figure S57. Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S58. Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 15(11Q22.1) MUTATED	8	22	1	19	0
DEL PEAK 15(11Q22.1) WILD-TYPE	29	18	9	31	25

Figure S58. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.1' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0024

Table S59. Gene #21: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 15(11Q22.1) MUTATED	8	11	25	6
DEL PEAK 15(11Q22.1) WILD-TYPE	24	54	19	15

Figure S59. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00465 (Fisher's exact test), Q value = 0.029

Table S60. Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 15(11Q22.1) MUTATED	11	12	22	5
DEL PEAK 15(11Q22.1) WILD-TYPE	23	52	21	16

Figure S60. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0073

Table S61. Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 15(11Q22.1) MUTATED	29	13	8
DEL PEAK 15(11Q22.1) WILD-TYPE	34	31	47

Figure S61. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0066

Table S62. Gene #21: 'del_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	54	18	24
DEL PEAK 15(11Q22.1) MUTATED	31	8	3	8
DEL PEAK 15(11Q22.1) WILD-TYPE	35	46	15	16

Figure S62. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0056

Table S63. Gene #21: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	50	16	33	29
DEL PEAK 15(11Q22.1) MUTATED	9	8	3	20	10
DEL PEAK 15(11Q22.1) WILD-TYPE	24	42	13	13	19

Figure S63. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00056

Table S64. Gene #21: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
DEL PEAK 15(11Q22.1) MUTATED	8	8	7	1	17	3	6
DEL PEAK 15(11Q22.1) WILD-TYPE	10	33	20	14	6	15	13

Figure S64. Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.1

Table S65. Gene #24: 'del_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 18(16Q21) MUTATED	4	1	0	0
DEL PEAK 18(16Q21) WILD-TYPE	30	63	43	21

Figure S65. Get High-res Image Gene #24: 'del_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0032

Table S66. Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 19(17P13.2) MUTATED	12	12	8	28	4
DEL PEAK 19(17P13.2) WILD-TYPE	25	28	2	22	21

Figure S66. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0073

Table S67. Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	45
DEL PEAK 19(17P13.2) MUTATED	9	42	13
DEL PEAK 19(17P13.2) WILD-TYPE	31	35	32

Figure S67. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00884 (Fisher's exact test), Q value = 0.044

Table S68. Gene #25: 'del_17p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 19(17P13.2) MUTATED	9	36	14	5
DEL PEAK 19(17P13.2) WILD-TYPE	23	29	30	16

Figure S68. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00627 (Fisher's exact test), Q value = 0.037

Table S69. Gene #25: 'del_17p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 19(17P13.2) MUTATED	10	36	13	5
DEL PEAK 19(17P13.2) WILD-TYPE	24	28	30	16

Figure S69. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.079

Table S70. Gene #25: 'del_17p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 19(17P13.2) MUTATED	21	13	30
DEL PEAK 19(17P13.2) WILD-TYPE	42	31	25

Figure S70. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00821 (Fisher's exact test), Q value = 0.043

Table S71. Gene #25: 'del_17p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	54	18	24
DEL PEAK 19(17P13.2) MUTATED	18	30	9	7
DEL PEAK 19(17P13.2) WILD-TYPE	48	24	9	17

Figure S71. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.1

Table S72. Gene #25: 'del_17p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
DEL PEAK 19(17P13.2) MUTATED	8	20	4	9	9	9	5
DEL PEAK 19(17P13.2) WILD-TYPE	10	21	23	6	14	9	14

Figure S72. Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0066

Table S73. Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 20(17Q11.2) MUTATED	6	7	4	23	2
DEL PEAK 20(17Q11.2) WILD-TYPE	31	33	6	27	23

Figure S73. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 0.037

Table S74. Gene #26: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	45
DEL PEAK 20(17Q11.2) MUTATED	4	28	10
DEL PEAK 20(17Q11.2) WILD-TYPE	36	49	35

Figure S74. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.092

Table S75. Gene #26: 'del_17q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	20	23	18
DEL PEAK 20(17Q11.2) MUTATED	4	6	8	0
DEL PEAK 20(17Q11.2) WILD-TYPE	12	14	15	18

Figure S75. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.11

Table S76. Gene #26: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 20(17Q11.2) MUTATED	5	25	9	3
DEL PEAK 20(17Q11.2) WILD-TYPE	27	40	35	18

Figure S76. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.017

Table S77. Gene #26: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 20(17Q11.2) MUTATED	6	27	6	3
DEL PEAK 20(17Q11.2) WILD-TYPE	28	37	37	18

Figure S77. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00782 (Fisher's exact test), Q value = 0.042

Table S78. Gene #26: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
DEL PEAK 20(17Q11.2) MUTATED	6	18	1	3	7	4	3
DEL PEAK 20(17Q11.2) WILD-TYPE	12	23	26	12	16	14	16

Figure S78. Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S79. Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 21(22Q13.31) MUTATED	18	5	9	29	4
DEL PEAK 21(22Q13.31) WILD-TYPE	19	35	1	21	21

Figure S79. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.051

Table S80. Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	45
DEL PEAK 21(22Q13.31) MUTATED	10	40	15
DEL PEAK 21(22Q13.31) WILD-TYPE	30	37	30

Figure S80. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.051

Table S81. Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 21(22Q13.31) MUTATED	8	36	13	8
DEL PEAK 21(22Q13.31) WILD-TYPE	24	29	31	13

Figure S81. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0052

Table S82. Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 21(22Q13.31) MUTATED	13	37	8	7
DEL PEAK 21(22Q13.31) WILD-TYPE	21	27	35	14

Figure S82. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0067 (Fisher's exact test), Q value = 0.038

Table S83. Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 21(22Q13.31) MUTATED	16	20	29
DEL PEAK 21(22Q13.31) WILD-TYPE	47	24	26

Figure S83. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.1

Table S84. Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	54	18	24
DEL PEAK 21(22Q13.31) MUTATED	18	29	7	11
DEL PEAK 21(22Q13.31) WILD-TYPE	48	25	11	13

Figure S84. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.14

Table S85. Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	50	16	33	29
DEL PEAK 21(22Q13.31) MUTATED	11	28	8	9	9
DEL PEAK 21(22Q13.31) WILD-TYPE	22	22	8	24	20

Figure S85. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0032

Table S86. Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
DEL PEAK 22(XP21.1) MUTATED	6	4	2	24	10
DEL PEAK 22(XP21.1) WILD-TYPE	31	36	8	26	15

Figure S86. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0066

Table S87. Gene #28: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	45
DEL PEAK 22(XP21.1) MUTATED	9	32	5
DEL PEAK 22(XP21.1) WILD-TYPE	31	45	40

Figure S87. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.14

Table S88. Gene #28: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	20	23	18
DEL PEAK 22(XP21.1) MUTATED	7	7	8	1
DEL PEAK 22(XP21.1) WILD-TYPE	9	13	15	17

Figure S88. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.12

Table S89. Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	65	44	21
DEL PEAK 22(XP21.1) MUTATED	10	25	9	2
DEL PEAK 22(XP21.1) WILD-TYPE	22	40	35	19

Figure S89. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.023

Table S90. Gene #28: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	64	43	21
DEL PEAK 22(XP21.1) MUTATED	7	27	11	1
DEL PEAK 22(XP21.1) WILD-TYPE	27	37	32	20

Figure S90. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.003

Table S91. Gene #28: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	44	55
DEL PEAK 22(XP21.1) MUTATED	12	7	27
DEL PEAK 22(XP21.1) WILD-TYPE	51	37	28

Figure S91. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.14

Table S92. Gene #28: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	54	18	24
DEL PEAK 22(XP21.1) MUTATED	15	21	7	3
DEL PEAK 22(XP21.1) WILD-TYPE	51	33	11	21

Figure S92. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.073

Table S93. Gene #28: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	18	41	27	15	23	18	19
DEL PEAK 22(XP21.1) MUTATED	3	19	6	5	5	7	1
DEL PEAK 22(XP21.1) WILD-TYPE	15	22	21	10	18	11	18

Figure S93. Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #10: '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/PCPG-TP/22533877/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/22542422/PCPG-TP.transferedmergedcluster.txt
Number of patients = 162
Number of significantly focal cnvs = 28
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

Download Results

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

References

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

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

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