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

Thyroid Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JW8CPJ

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 30 focal events and 10 molecular subtypes across 494 patients, 88 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_xq22.3 cnv correlated to 'CN_CNMF'.
del_1q24.2 cnv correlated to 'CN_CNMF'.
del_2p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q35 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' and 'MIRSEQ_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF'.
del_8p22 cnv correlated to 'CN_CNMF'.
del_8p12 cnv correlated to 'CN_CNMF'.
del_8q24.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.13 cnv correlated to 'CN_CNMF'.
del_10q21.2 cnv correlated to 'CN_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_13q12.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
del_13q21.31 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_15q25.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18p11.21 cnv correlated to 'CN_CNMF'.
del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q21.1 cnv correlated to 'CN_CNMF'.
del_22q13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 30 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, 88 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 2p23 1	12 (2%)	482	1e-05 (0.00288)	1e-05 (0.00288)	0.77 (1.00)	0.0921 (1.00)	3e-05 (0.00744)	3e-05 (0.00744)	1e-05 (0.00288)	1e-05 (0.00288)	2e-05 (0.0051)	1e-05 (0.00288)
del 2q35	12 (2%)	482	1e-05 (0.00288)	1e-05 (0.00288)	0.539 (1.00)	0.023 (1.00)	3e-05 (0.00744)	1e-05 (0.00288)	1e-05 (0.00288)	2e-05 (0.0051)	1e-05 (0.00288)	1e-05 (0.00288)
del 22q13 1	86 (17%)	408	1e-05 (0.00288)	1e-05 (0.00288)	0.119 (1.00)	0.504 (1.00)	1e-05 (0.00288)	1e-05 (0.00288)	0.00081 (0.168)	0.00013 (0.0305)	1e-05 (0.00288)	2e-05 (0.0051)
del 22q13 2	86 (17%)	408	1e-05 (0.00288)	2e-05 (0.0051)	0.119 (1.00)	0.504 (1.00)	1e-05 (0.00288)	1e-05 (0.00288)	0.0011 (0.222)	0.00011 (0.026)	1e-05 (0.00288)	3e-05 (0.00744)
del 22q13 31	86 (17%)	408	1e-05 (0.00288)	3e-05 (0.00744)	0.118 (1.00)	0.501 (1.00)	1e-05 (0.00288)	1e-05 (0.00288)	0.00089 (0.184)	0.00017 (0.0393)	2e-05 (0.0051)	1e-05 (0.00288)
del 22q13 32	87 (18%)	407	1e-05 (0.00288)	1e-05 (0.00288)	0.118 (1.00)	0.502 (1.00)	1e-05 (0.00288)	1e-05 (0.00288)	0.00051 (0.111)	8e-05 (0.019)	2e-05 (0.0051)	1e-05 (0.00288)
del 8q24 22	7 (1%)	487	7e-05 (0.0167)	0.00046 (0.101)	0.838 (1.00)	0.172 (1.00)	0.00172 (0.335)	0.00045 (0.0994)	0.0002 (0.046)	0.00173 (0.336)	0.00068 (0.145)	0.00014 (0.0328)
del 10q23 31	12 (2%)	482	1e-05 (0.00288)	0.0023 (0.435)	0.0515 (1.00)	0.149 (1.00)	0.00066 (0.141)	0.00071 (0.15)	0.00458 (0.82)	0.00043 (0.0955)	0.00042 (0.0937)	0.0008 (0.167)
del 19p13 2	7 (1%)	487	0.00071 (0.15)	0.00048 (0.105)	0.856 (1.00)	0.299 (1.00)	0.00171 (0.335)	0.00027 (0.0607)	0.00022 (0.0499)	0.00186 (0.357)	0.0009 (0.185)	0.00021 (0.0481)
del 15q25 3	9 (2%)	485	0.00021 (0.0481)	0.0014 (0.279)	0.243 (1.00)	0.0618 (1.00)	0.0049 (0.862)	0.00106 (0.216)	0.00069 (0.146)	0.00016 (0.0371)	0.00153 (0.303)	0.00045 (0.0994)
del 6q22 31	7 (1%)	487	6e-05 (0.0144)	0.00222 (0.422)	0.0126 (1.00)	0.574 (1.00)	0.0321 (1.00)	0.0138 (1.00)	0.00327 (0.605)	0.00092 (0.189)	0.00971 (1.00)	0.00181 (0.349)
del 11p15 1	7 (1%)	487	1e-05 (0.00288)	0.0115 (1.00)	0.494 (1.00)	0.958 (1.00)	0.00657 (1.00)	0.0138 (1.00)	0.00312 (0.583)	0.00117 (0.235)	0.00982 (1.00)	0.00312 (0.583)
del 13q12 3	16 (3%)	478	0.00606 (1.00)	0.0006 (0.129)	0.184 (1.00)	0.085 (1.00)	0.00051 (0.111)	0.0104 (1.00)	0.0349 (1.00)	0.00537 (0.934)	0.0118 (1.00)	0.0066 (1.00)
del 13q21 31	18 (4%)	476	0.00528 (0.924)	0.0167 (1.00)	0.0553 (1.00)	0.186 (1.00)	0.00106 (0.216)	0.00159 (0.313)	0.00452 (0.814)	0.00015 (0.0349)	0.00485 (0.858)	0.00469 (0.835)
amp xq22 3	15 (3%)	479	2e-05 (0.0051)	0.717 (1.00)	0.841 (1.00)	0.504 (1.00)	0.774 (1.00)	0.988 (1.00)	1 (1.00)	0.713 (1.00)	0.945 (1.00)	0.902 (1.00)
del 1q24 2	3 (1%)	491	0.00037 (0.0829)	0.0488 (1.00)			0.0959 (1.00)	0.111 (1.00)	0.0281 (1.00)	0.0164 (1.00)	0.0701 (1.00)	0.0283 (1.00)
del 8p23 2	4 (1%)	490	1e-05 (0.00288)	0.0187 (1.00)			0.0421 (1.00)	0.0355 (1.00)	0.00858 (1.00)	0.0037 (0.681)	0.0229 (1.00)	0.00973 (1.00)
del 8p22	4 (1%)	490	3e-05 (0.00744)	0.0182 (1.00)			0.0431 (1.00)	0.0376 (1.00)	0.00818 (1.00)	0.00379 (0.694)	0.0228 (1.00)	0.00942 (1.00)
del 8p12	4 (1%)	490	3e-05 (0.00744)	0.0187 (1.00)			0.0437 (1.00)	0.0368 (1.00)	0.00861 (1.00)	0.00396 (0.721)	0.0224 (1.00)	0.00918 (1.00)
del 9q21 13	24 (5%)	470	1e-05 (0.00288)	0.0567 (1.00)	0.174 (1.00)	0.115 (1.00)	0.104 (1.00)	0.0397 (1.00)	0.00909 (1.00)	0.00441 (0.798)	0.0123 (1.00)	0.00246 (0.462)
del 10q21 2	12 (2%)	482	5e-05 (0.012)	0.0654 (1.00)	0.157 (1.00)	0.675 (1.00)	0.0185 (1.00)	0.0153 (1.00)	0.136 (1.00)	0.174 (1.00)	0.0352 (1.00)	0.18 (1.00)
del 18p11 21	4 (1%)	490	0.00023 (0.052)	0.183 (1.00)	1 (1.00)	0.386 (1.00)	0.238 (1.00)	0.161 (1.00)	0.113 (1.00)	0.0642 (1.00)	0.0229 (1.00)	0.207 (1.00)
del 21q21 1	9 (2%)	485	6e-05 (0.0144)	0.31 (1.00)	0.147 (1.00)	0.323 (1.00)	0.739 (1.00)	0.709 (1.00)	0.0536 (1.00)	0.119 (1.00)	0.0536 (1.00)	0.0212 (1.00)
del 5p15 2	4 (1%)	490	0.347 (1.00)	0.366 (1.00)			0.413 (1.00)	0.541 (1.00)	0.556 (1.00)	0.689 (1.00)	0.48 (1.00)	0.164 (1.00)
del 7q34	4 (1%)	490	0.639 (1.00)	0.794 (1.00)			0.737 (1.00)	0.816 (1.00)	0.689 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
del 16q23 3	6 (1%)	488	0.0489 (1.00)	0.12 (1.00)	0.444 (1.00)	0.445 (1.00)	0.287 (1.00)	0.101 (1.00)	0.198 (1.00)	0.211 (1.00)	0.295 (1.00)	0.26 (1.00)
del 17p13 1	8 (2%)	486	0.00186 (0.357)	0.416 (1.00)	1 (1.00)	0.389 (1.00)	0.651 (1.00)	0.647 (1.00)	0.329 (1.00)	0.141 (1.00)	0.674 (1.00)	0.192 (1.00)
del 18q22 2	5 (1%)	489	0.00135 (0.27)	0.0593 (1.00)	1 (1.00)	0.505 (1.00)	0.116 (1.00)	0.0615 (1.00)	0.041 (1.00)	0.0188 (1.00)	0.0077 (1.00)	0.0642 (1.00)
del xq22 1	6 (1%)	488	0.0741 (1.00)	0.421 (1.00)	0.0983 (1.00)	0.228 (1.00)	0.59 (1.00)	0.557 (1.00)	0.528 (1.00)	0.446 (1.00)	0.701 (1.00)	0.472 (1.00)
del xq22 3	4 (1%)	490	0.054 (1.00)	0.0459 (1.00)	0.276 (1.00)	0.195 (1.00)	0.092 (1.00)	0.279 (1.00)	0.114 (1.00)	0.0645 (1.00)	0.227 (1.00)	0.207 (1.00)

'amp_xq22.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S1. Gene #1: 'amp_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
AMP PEAK 1(XQ22.3) MUTATED	7	8	0
AMP PEAK 1(XQ22.3) WILD-TYPE	27	375	77

Figure S1. Get High-res Image Gene #1: 'amp_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q24.2' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.083

Table S2. Gene #2: 'del_1q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 1(1Q24.2) MUTATED	3	0	0
DEL PEAK 1(1Q24.2) WILD-TYPE	31	383	77

Figure S2. Get High-res Image Gene #2: 'del_1q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S3. Gene #3: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 2(2P23.1) MUTATED	9	1	2
DEL PEAK 2(2P23.1) WILD-TYPE	25	382	75

Figure S3. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S4. Gene #3: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	151	70
DEL PEAK 2(2P23.1) MUTATED	0	11	1
DEL PEAK 2(2P23.1) WILD-TYPE	273	140	69

Figure S4. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p23.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0074

Table S5. Gene #3: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
DEL PEAK 2(2P23.1) MUTATED	12	0	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	142	55	116	167

Figure S5. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0074

Table S6. Gene #3: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 2(2P23.1) MUTATED	11	1	0	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	115	99	73	115	78

Figure S6. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S7. Gene #3: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
DEL PEAK 2(2P23.1) MUTATED	12	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	138	173	170

Figure S7. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S8. Gene #3: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 2(2P23.1) MUTATED	11	1	0
DEL PEAK 2(2P23.1) WILD-TYPE	114	204	163

Figure S8. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S9. Gene #3: 'del_2p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
DEL PEAK 2(2P23.1) MUTATED	12	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	151	169	161

Figure S9. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S10. Gene #3: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 2(2P23.1) MUTATED	12	0	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	111	187	105	78

Figure S10. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q35' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S11. Gene #4: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 3(2Q35) MUTATED	11	1	0
DEL PEAK 3(2Q35) WILD-TYPE	23	382	77

Figure S11. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q35' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S12. Gene #4: 'del_2q35' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	151	70
DEL PEAK 3(2Q35) MUTATED	0	12	0
DEL PEAK 3(2Q35) WILD-TYPE	273	139	70

Figure S12. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q35' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0074

Table S13. Gene #4: 'del_2q35' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
DEL PEAK 3(2Q35) MUTATED	12	0	0	0
DEL PEAK 3(2Q35) WILD-TYPE	142	55	116	167

Figure S13. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q35' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S14. Gene #4: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 3(2Q35) MUTATED	12	0	0	0	0
DEL PEAK 3(2Q35) WILD-TYPE	114	100	73	115	78

Figure S14. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q35' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S15. Gene #4: 'del_2q35' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
DEL PEAK 3(2Q35) MUTATED	12	0	0
DEL PEAK 3(2Q35) WILD-TYPE	138	173	170

Figure S15. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q35' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S16. Gene #4: 'del_2q35' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 3(2Q35) MUTATED	11	1	0
DEL PEAK 3(2Q35) WILD-TYPE	114	204	163

Figure S16. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q35' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S17. Gene #4: 'del_2q35' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
DEL PEAK 3(2Q35) MUTATED	12	0	0
DEL PEAK 3(2Q35) WILD-TYPE	151	169	161

Figure S17. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q35' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S18. Gene #4: 'del_2q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 3(2Q35) MUTATED	12	0	0	0
DEL PEAK 3(2Q35) WILD-TYPE	111	187	105	78

Figure S18. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S19. Gene #6: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 6(6Q22.31) MUTATED	5	2	0
DEL PEAK 6(6Q22.31) WILD-TYPE	29	381	77

Figure S19. Get High-res Image Gene #6: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.19

Table S20. Gene #6: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 6(6Q22.31) MUTATED	6	0	1
DEL PEAK 6(6Q22.31) WILD-TYPE	119	205	162

Figure S20. Get High-res Image Gene #6: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S21. Gene #8: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 9(8P23.2) MUTATED	4	0	0
DEL PEAK 9(8P23.2) WILD-TYPE	30	383	77

Figure S21. Get High-res Image Gene #8: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p22' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0074

Table S22. Gene #9: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 10(8P22) MUTATED	4	0	0
DEL PEAK 10(8P22) WILD-TYPE	30	383	77

Figure S22. Get High-res Image Gene #9: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0074

Table S23. Gene #10: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 11(8P12) MUTATED	4	0	0
DEL PEAK 11(8P12) WILD-TYPE	30	383	77

Figure S23. Get High-res Image Gene #10: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_8q24.22' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.017

Table S24. Gene #11: 'del_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 12(8Q24.22) MUTATED	5	2	0
DEL PEAK 12(8Q24.22) WILD-TYPE	29	381	77

Figure S24. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8q24.22' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.1

Table S25. Gene #11: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	151	70
DEL PEAK 12(8Q24.22) MUTATED	0	7	0
DEL PEAK 12(8Q24.22) WILD-TYPE	273	144	70

Figure S25. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.099

Table S26. Gene #11: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 12(8Q24.22) MUTATED	7	0	0	0	0
DEL PEAK 12(8Q24.22) WILD-TYPE	119	100	73	115	78

Figure S26. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.22' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.046

Table S27. Gene #11: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
DEL PEAK 12(8Q24.22) MUTATED	7	0	0
DEL PEAK 12(8Q24.22) WILD-TYPE	143	173	170

Figure S27. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.14

Table S28. Gene #11: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
DEL PEAK 12(8Q24.22) MUTATED	7	0	0
DEL PEAK 12(8Q24.22) WILD-TYPE	156	169	161

Figure S28. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.033

Table S29. Gene #11: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 12(8Q24.22) MUTATED	7	0	0	0
DEL PEAK 12(8Q24.22) WILD-TYPE	116	187	105	78

Figure S29. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S30. Gene #12: 'del_9q21.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 13(9Q21.13) MUTATED	16	7	1
DEL PEAK 13(9Q21.13) WILD-TYPE	18	376	76

Figure S30. Get High-res Image Gene #12: 'del_9q21.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S31. Gene #13: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 14(10Q21.2) MUTATED	6	6	0
DEL PEAK 14(10Q21.2) WILD-TYPE	28	377	77

Figure S31. Get High-res Image Gene #13: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S32. Gene #14: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 15(10Q23.31) MUTATED	7	5	0
DEL PEAK 15(10Q23.31) WILD-TYPE	27	378	77

Figure S32. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.14

Table S33. Gene #14: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
DEL PEAK 15(10Q23.31) MUTATED	10	0	2	0
DEL PEAK 15(10Q23.31) WILD-TYPE	144	55	114	167

Figure S33. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.15

Table S34. Gene #14: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 15(10Q23.31) MUTATED	9	3	0	0	0
DEL PEAK 15(10Q23.31) WILD-TYPE	117	97	73	115	78

Figure S34. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.095

Table S35. Gene #14: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 15(10Q23.31) MUTATED	9	1	2
DEL PEAK 15(10Q23.31) WILD-TYPE	116	204	161

Figure S35. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.094

Table S36. Gene #14: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
DEL PEAK 15(10Q23.31) MUTATED	10	0	2
DEL PEAK 15(10Q23.31) WILD-TYPE	153	169	159

Figure S36. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.17

Table S37. Gene #14: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 15(10Q23.31) MUTATED	9	1	2	0
DEL PEAK 15(10Q23.31) WILD-TYPE	114	186	103	78

Figure S37. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S38. Gene #15: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 16(11P15.1) MUTATED	6	0	1
DEL PEAK 16(11P15.1) WILD-TYPE	28	383	76

Figure S38. Get High-res Image Gene #15: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.24

Table S39. Gene #15: 'del_11p15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 16(11P15.1) MUTATED	6	0	1
DEL PEAK 16(11P15.1) WILD-TYPE	119	205	162

Figure S39. Get High-res Image Gene #15: 'del_11p15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.3' versus 'METHLYATION_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.13

Table S40. Gene #16: 'del_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	151	70
DEL PEAK 17(13Q12.3) MUTATED	2	11	3
DEL PEAK 17(13Q12.3) WILD-TYPE	271	140	67

Figure S40. Get High-res Image Gene #16: 'del_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.3' versus 'MRNASEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.11

Table S41. Gene #16: 'del_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
DEL PEAK 17(13Q12.3) MUTATED	11	3	2	0
DEL PEAK 17(13Q12.3) WILD-TYPE	143	52	114	167

Figure S41. Get High-res Image Gene #16: 'del_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q21.31' versus 'MRNASEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.22

Table S42. Gene #17: 'del_13q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
DEL PEAK 18(13Q21.31) MUTATED	11	2	5	0
DEL PEAK 18(13Q21.31) WILD-TYPE	143	53	111	167

Figure S42. Get High-res Image Gene #17: 'del_13q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.035

Table S43. Gene #17: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 18(13Q21.31) MUTATED	11	7	0
DEL PEAK 18(13Q21.31) WILD-TYPE	114	198	163

Figure S43. Get High-res Image Gene #17: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q25.3' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.048

Table S44. Gene #18: 'del_15q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 19(15Q25.3) MUTATED	5	3	1
DEL PEAK 19(15Q25.3) WILD-TYPE	29	380	76

Figure S44. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.22

Table S45. Gene #18: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 19(15Q25.3) MUTATED	8	0	0	1	0
DEL PEAK 19(15Q25.3) WILD-TYPE	118	100	73	114	78

Figure S45. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.15

Table S46. Gene #18: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
DEL PEAK 19(15Q25.3) MUTATED	8	1	0
DEL PEAK 19(15Q25.3) WILD-TYPE	142	172	170

Figure S46. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.037

Table S47. Gene #18: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 19(15Q25.3) MUTATED	8	1	0
DEL PEAK 19(15Q25.3) WILD-TYPE	117	204	163

Figure S47. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.099

Table S48. Gene #18: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 19(15Q25.3) MUTATED	8	1	0	0
DEL PEAK 19(15Q25.3) WILD-TYPE	115	186	105	78

Figure S48. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18p11.21' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.052

Table S49. Gene #21: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 23(18P11.21) MUTATED	3	0	1
DEL PEAK 23(18P11.21) WILD-TYPE	31	383	76

Figure S49. Get High-res Image Gene #21: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'CN_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.15

Table S50. Gene #23: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 25(19P13.2) MUTATED	4	2	1
DEL PEAK 25(19P13.2) WILD-TYPE	30	381	76

Figure S50. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.1

Table S51. Gene #23: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	151	70
DEL PEAK 25(19P13.2) MUTATED	0	7	0
DEL PEAK 25(19P13.2) WILD-TYPE	273	144	70

Figure S51. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.061

Table S52. Gene #23: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 25(19P13.2) MUTATED	7	0	0	0	0
DEL PEAK 25(19P13.2) WILD-TYPE	119	100	73	115	78

Figure S52. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.05

Table S53. Gene #23: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
DEL PEAK 25(19P13.2) MUTATED	7	0	0
DEL PEAK 25(19P13.2) WILD-TYPE	143	173	170

Figure S53. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.19

Table S54. Gene #23: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
DEL PEAK 25(19P13.2) MUTATED	7	0	0
DEL PEAK 25(19P13.2) WILD-TYPE	156	169	161

Figure S54. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.048

Table S55. Gene #23: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 25(19P13.2) MUTATED	7	0	0	0
DEL PEAK 25(19P13.2) WILD-TYPE	116	187	105	78

Figure S55. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q21.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S56. Gene #24: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 28(21Q21.1) MUTATED	5	2	2
DEL PEAK 28(21Q21.1) WILD-TYPE	29	381	75

Figure S56. Get High-res Image Gene #24: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S57. Gene #25: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 29(22Q13.1) MUTATED	9	0	77
DEL PEAK 29(22Q13.1) WILD-TYPE	25	383	0

Figure S57. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S58. Gene #25: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	151	70
DEL PEAK 29(22Q13.1) MUTATED	35	45	6
DEL PEAK 29(22Q13.1) WILD-TYPE	238	106	64

Figure S58. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S59. Gene #25: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
DEL PEAK 29(22Q13.1) MUTATED	45	8	26	7
DEL PEAK 29(22Q13.1) WILD-TYPE	109	47	90	160

Figure S59. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S60. Gene #25: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 29(22Q13.1) MUTATED	40	13	22	9	2
DEL PEAK 29(22Q13.1) WILD-TYPE	86	87	51	106	76

Figure S60. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.17

Table S61. Gene #25: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
DEL PEAK 29(22Q13.1) MUTATED	41	24	21
DEL PEAK 29(22Q13.1) WILD-TYPE	109	149	149

Figure S61. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.031

Table S62. Gene #25: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 29(22Q13.1) MUTATED	38	28	20
DEL PEAK 29(22Q13.1) WILD-TYPE	87	177	143

Figure S62. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S63. Gene #25: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
DEL PEAK 29(22Q13.1) MUTATED	49	18	19
DEL PEAK 29(22Q13.1) WILD-TYPE	114	151	142

Figure S63. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S64. Gene #25: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 29(22Q13.1) MUTATED	38	26	18	4
DEL PEAK 29(22Q13.1) WILD-TYPE	85	161	87	74

Figure S64. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S65. Gene #26: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 30(22Q13.2) MUTATED	9	0	77
DEL PEAK 30(22Q13.2) WILD-TYPE	25	383	0

Figure S65. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S66. Gene #26: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	151	70
DEL PEAK 30(22Q13.2) MUTATED	35	45	6
DEL PEAK 30(22Q13.2) WILD-TYPE	238	106	64

Figure S66. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S67. Gene #26: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
DEL PEAK 30(22Q13.2) MUTATED	45	8	26	7
DEL PEAK 30(22Q13.2) WILD-TYPE	109	47	90	160

Figure S67. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S68. Gene #26: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 30(22Q13.2) MUTATED	40	13	22	9	2
DEL PEAK 30(22Q13.2) WILD-TYPE	86	87	51	106	76

Figure S68. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.2' versus 'MIRSEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.22

Table S69. Gene #26: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
DEL PEAK 30(22Q13.2) MUTATED	41	24	21
DEL PEAK 30(22Q13.2) WILD-TYPE	109	149	149

Figure S69. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.026

Table S70. Gene #26: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 30(22Q13.2) MUTATED	38	28	20
DEL PEAK 30(22Q13.2) WILD-TYPE	87	177	143

Figure S70. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S71. Gene #26: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
DEL PEAK 30(22Q13.2) MUTATED	49	18	19
DEL PEAK 30(22Q13.2) WILD-TYPE	114	151	142

Figure S71. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0074

Table S72. Gene #26: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 30(22Q13.2) MUTATED	38	26	18	4
DEL PEAK 30(22Q13.2) WILD-TYPE	85	161	87	74

Figure S72. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S73. Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 31(22Q13.31) MUTATED	9	0	77
DEL PEAK 31(22Q13.31) WILD-TYPE	25	383	0

Figure S73. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0074

Table S74. Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	151	70
DEL PEAK 31(22Q13.31) MUTATED	35	45	6
DEL PEAK 31(22Q13.31) WILD-TYPE	238	106	64

Figure S74. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S75. Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
DEL PEAK 31(22Q13.31) MUTATED	45	8	26	7
DEL PEAK 31(22Q13.31) WILD-TYPE	109	47	90	160

Figure S75. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S76. Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 31(22Q13.31) MUTATED	40	13	22	9	2
DEL PEAK 31(22Q13.31) WILD-TYPE	86	87	51	106	76

Figure S76. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.18

Table S77. Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
DEL PEAK 31(22Q13.31) MUTATED	41	24	21
DEL PEAK 31(22Q13.31) WILD-TYPE	109	149	149

Figure S77. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.039

Table S78. Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 31(22Q13.31) MUTATED	38	28	20
DEL PEAK 31(22Q13.31) WILD-TYPE	87	177	143

Figure S78. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S79. Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
DEL PEAK 31(22Q13.31) MUTATED	49	18	19
DEL PEAK 31(22Q13.31) WILD-TYPE	114	151	142

Figure S79. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S80. Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 31(22Q13.31) MUTATED	38	26	18	4
DEL PEAK 31(22Q13.31) WILD-TYPE	85	161	87	74

Figure S80. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S81. Gene #28: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
DEL PEAK 32(22Q13.32) MUTATED	9	1	77
DEL PEAK 32(22Q13.32) WILD-TYPE	25	382	0

Figure S81. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S82. Gene #28: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	151	70
DEL PEAK 32(22Q13.32) MUTATED	35	46	6
DEL PEAK 32(22Q13.32) WILD-TYPE	238	105	64

Figure S82. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S83. Gene #28: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
DEL PEAK 32(22Q13.32) MUTATED	46	8	26	7
DEL PEAK 32(22Q13.32) WILD-TYPE	108	47	90	160

Figure S83. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S84. Gene #28: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	126	100	73	115	78
DEL PEAK 32(22Q13.32) MUTATED	41	13	22	9	2
DEL PEAK 32(22Q13.32) WILD-TYPE	85	87	51	106	76

Figure S84. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.11

Table S85. Gene #28: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
DEL PEAK 32(22Q13.32) MUTATED	42	24	21
DEL PEAK 32(22Q13.32) WILD-TYPE	108	149	149

Figure S85. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S86. Gene #28: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	205	163
DEL PEAK 32(22Q13.32) MUTATED	39	28	20
DEL PEAK 32(22Q13.32) WILD-TYPE	86	177	143

Figure S86. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S87. Gene #28: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
DEL PEAK 32(22Q13.32) MUTATED	50	18	19
DEL PEAK 32(22Q13.32) WILD-TYPE	113	151	142

Figure S87. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S88. Gene #28: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	123	187	105	78
DEL PEAK 32(22Q13.32) MUTATED	39	26	18	4
DEL PEAK 32(22Q13.32) WILD-TYPE	84	161	87	74

Figure S88. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = THCA-TP.transferedmergedcluster.txt
Number of patients = 494
Number of significantly focal cnvs = 30
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)

Made with Nozzle