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

Adrenocortical Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13777J4

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 46 focal events and 10 molecular subtypes across 90 patients, 29 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q22 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_4q35.1 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_12q14.1 cnv correlated to 'CN_CNMF'.
amp_14q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_16p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_16q22.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_16q24.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_19p13.12 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_xp11.22 cnv correlated to 'CN_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF'.
del_4q34.3 cnv correlated to 'MIRSEQ_MATURE_CNMF'.
del_4q34.3 cnv correlated to 'MIRSEQ_MATURE_CNMF'.
del_9p23 cnv correlated to 'MRNASEQ_CNMF'.
del_9p21.3 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 46 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, 29 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
amp 14q11 2	27 (30%)	63	0.0001 (0.0443)	0.0133 (1.00)	0.0221 (1.00)	0.0288 (1.00)	3e-05 (0.0133)	1e-05 (0.00458)	0.00032 (0.139)	0.00687 (1.00)	0.00067 (0.287)	0.00102 (0.429)
amp 5q35 3	63 (70%)	27	1e-05 (0.00458)	0.00132 (0.549)	0.192 (1.00)	0.00694 (1.00)	1e-05 (0.00458)	1e-05 (0.00458)	0.00632 (1.00)	0.0478 (1.00)	0.0119 (1.00)	0.291 (1.00)
amp 16p13 3	50 (56%)	40	1e-05 (0.00458)	0.263 (1.00)	0.931 (1.00)	0.0539 (1.00)	0.00017 (0.0745)	1e-05 (0.00458)	0.076 (1.00)	0.00965 (1.00)	0.0528 (1.00)	0.584 (1.00)
amp 16q24 2	49 (54%)	41	1e-05 (0.00458)	0.0273 (1.00)	0.954 (1.00)	0.323 (1.00)	0.0003 (0.131)	1e-05 (0.00458)	0.063 (1.00)	0.00281 (1.00)	0.00515 (1.00)	0.38 (1.00)
amp 1q22	17 (19%)	73	0.00833 (1.00)	0.00038 (0.164)	0.563 (1.00)	0.398 (1.00)	0.00251 (1.00)	0.00019 (0.083)	0.116 (1.00)	0.156 (1.00)	0.0136 (1.00)	0.44 (1.00)
amp 16q22 1	56 (62%)	34	1e-05 (0.00458)	0.371 (1.00)	0.923 (1.00)	0.804 (1.00)	0.0293 (1.00)	0.00016 (0.0702)	0.066 (1.00)	0.0224 (1.00)	0.153 (1.00)	0.86 (1.00)
amp 19p13 12	58 (64%)	32	0.00046 (0.198)	0.034 (1.00)	0.19 (1.00)	0.00967 (1.00)	0.00194 (0.795)	0.00038 (0.164)	0.325 (1.00)	0.48 (1.00)	0.584 (1.00)	0.172 (1.00)
del 9p21 3	27 (30%)	63	0.00709 (1.00)	0.00362 (1.00)	0.167 (1.00)	0.224 (1.00)	2e-05 (0.00894)	0.00032 (0.139)	0.0171 (1.00)	0.181 (1.00)	0.0088 (1.00)	0.567 (1.00)
amp 4q35 1	29 (32%)	61	2e-05 (0.00894)	0.197 (1.00)	0.766 (1.00)	0.559 (1.00)	0.00081 (0.344)	0.00088 (0.373)	0.0562 (1.00)	0.00109 (0.457)	0.0677 (1.00)	0.296 (1.00)
amp 5p15 33	65 (72%)	25	1e-05 (0.00458)	0.883 (1.00)	0.455 (1.00)	0.89 (1.00)	0.00998 (1.00)	0.00088 (0.373)	0.0444 (1.00)	0.18 (1.00)	0.0159 (1.00)	0.305 (1.00)
amp 12q14 1	70 (78%)	20	1e-05 (0.00458)	0.283 (1.00)	0.0197 (1.00)	0.0105 (1.00)	0.0224 (1.00)	0.0019 (0.781)	0.459 (1.00)	0.488 (1.00)	0.351 (1.00)	0.0905 (1.00)
amp xp11 22	49 (54%)	41	0.00015 (0.066)	0.92 (1.00)	0.435 (1.00)	0.017 (1.00)	0.0334 (1.00)	0.0963 (1.00)	0.764 (1.00)	0.144 (1.00)	0.74 (1.00)	0.0889 (1.00)
amp xq28	46 (51%)	44	0.00037 (0.16)	0.757 (1.00)	0.216 (1.00)	0.0448 (1.00)	0.00882 (1.00)	0.0114 (1.00)	0.512 (1.00)	0.261 (1.00)	1 (1.00)	0.0295 (1.00)
del 4q34 3	25 (28%)	65	0.0011 (0.46)	0.0643 (1.00)	0.864 (1.00)	0.637 (1.00)	0.0218 (1.00)	0.039 (1.00)	0.0372 (1.00)	0.0418 (1.00)	0.00011 (0.0486)	0.248 (1.00)
del 4q34 3	28 (31%)	62	0.00146 (0.604)	0.00485 (1.00)	0.731 (1.00)	0.148 (1.00)	0.185 (1.00)	0.189 (1.00)	0.0897 (1.00)	0.187 (1.00)	0.00012 (0.0529)	0.263 (1.00)
del 9p23	24 (27%)	66	0.00909 (1.00)	0.00832 (1.00)	0.155 (1.00)	0.0504 (1.00)	3e-05 (0.0133)	0.00138 (0.573)	0.00748 (1.00)	0.172 (1.00)	0.00804 (1.00)	0.731 (1.00)
amp 4p16 3	41 (46%)	49	0.00075 (0.32)	0.547 (1.00)	0.914 (1.00)	0.19 (1.00)	0.0132 (1.00)	0.00575 (1.00)	0.488 (1.00)	0.0459 (1.00)	0.408 (1.00)	0.953 (1.00)
amp 6p21 31	19 (21%)	71	0.0648 (1.00)	0.798 (1.00)	1 (1.00)	0.801 (1.00)	0.0811 (1.00)	1 (1.00)	0.141 (1.00)	0.0266 (1.00)	0.404 (1.00)	0.303 (1.00)
amp 6q24 3	19 (21%)	71	0.0227 (1.00)	0.909 (1.00)	0.965 (1.00)	0.638 (1.00)	0.0465 (1.00)	0.934 (1.00)	0.671 (1.00)	0.234 (1.00)	0.631 (1.00)	1 (1.00)
amp 7p22 1	54 (60%)	36	0.00199 (0.812)	0.484 (1.00)	0.425 (1.00)	0.675 (1.00)	0.00749 (1.00)	0.0331 (1.00)	0.57 (1.00)	0.491 (1.00)	0.806 (1.00)	0.133 (1.00)
amp 9q31 3	34 (38%)	56	0.00059 (0.253)	0.0202 (1.00)	0.229 (1.00)	0.137 (1.00)	0.0289 (1.00)	0.0176 (1.00)	0.0567 (1.00)	0.199 (1.00)	0.251 (1.00)	0.129 (1.00)
amp 17q25 3	18 (20%)	72	0.0337 (1.00)	0.69 (1.00)	0.575 (1.00)	0.1 (1.00)	0.128 (1.00)	0.672 (1.00)	0.398 (1.00)	0.695 (1.00)	0.304 (1.00)	0.466 (1.00)
amp 19q12	56 (62%)	34	0.00104 (0.437)	0.0202 (1.00)	0.396 (1.00)	0.165 (1.00)	0.00189 (0.779)	0.00098 (0.414)	0.198 (1.00)	0.253 (1.00)	0.513 (1.00)	0.0629 (1.00)
del 1p36 23	38 (42%)	52	0.0226 (1.00)	0.00399 (1.00)	0.566 (1.00)	0.148 (1.00)	0.0712 (1.00)	0.00372 (1.00)	0.833 (1.00)	0.558 (1.00)	0.405 (1.00)	0.826 (1.00)
del 1q43	18 (20%)	72	0.015 (1.00)	0.0454 (1.00)	0.164 (1.00)	0.159 (1.00)	0.591 (1.00)	0.14 (1.00)	0.524 (1.00)	0.555 (1.00)	0.192 (1.00)	0.181 (1.00)
del 2q22 1	18 (20%)	72	0.039 (1.00)	0.00369 (1.00)	0.624 (1.00)	0.794 (1.00)	0.239 (1.00)	0.09 (1.00)	0.314 (1.00)	0.664 (1.00)	0.407 (1.00)	0.489 (1.00)
del 2q37 3	21 (23%)	69	0.006 (1.00)	0.0266 (1.00)	0.689 (1.00)	0.831 (1.00)	0.297 (1.00)	0.0916 (1.00)	0.482 (1.00)	0.529 (1.00)	0.569 (1.00)	0.938 (1.00)
del 3q13 31	25 (28%)	65	0.3 (1.00)	0.0454 (1.00)	0.419 (1.00)	0.473 (1.00)	0.157 (1.00)	0.0401 (1.00)	0.45 (1.00)	0.2 (1.00)	0.85 (1.00)	0.37 (1.00)
del 4q35 1	30 (33%)	60	0.00543 (1.00)	0.0124 (1.00)	0.458 (1.00)	0.388 (1.00)	0.0955 (1.00)	0.0424 (1.00)	0.192 (1.00)	0.166 (1.00)	0.00077 (0.328)	0.682 (1.00)
del 6p24 3	20 (22%)	70	0.109 (1.00)	0.918 (1.00)	0.578 (1.00)	0.319 (1.00)	0.622 (1.00)	0.481 (1.00)	1 (1.00)	0.0985 (1.00)	1 (1.00)	0.459 (1.00)
del 6q26	21 (23%)	69	0.119 (1.00)	0.859 (1.00)	0.671 (1.00)	0.316 (1.00)	0.322 (1.00)	0.307 (1.00)	0.505 (1.00)	0.347 (1.00)	0.224 (1.00)	0.594 (1.00)
del 7q36 3	11 (12%)	79	0.0382 (1.00)	0.256 (1.00)	0.533 (1.00)	0.663 (1.00)	0.177 (1.00)	0.339 (1.00)	0.896 (1.00)	0.736 (1.00)	0.0962 (1.00)	0.245 (1.00)
del 10q23 1	11 (12%)	79	0.257 (1.00)	0.259 (1.00)	1 (1.00)	0.238 (1.00)	0.236 (1.00)	0.747 (1.00)	1 (1.00)	0.969 (1.00)	1 (1.00)	0.287 (1.00)
del 11p15 5	27 (30%)	63	0.00741 (1.00)	0.0199 (1.00)	0.458 (1.00)	0.673 (1.00)	0.0891 (1.00)	0.0333 (1.00)	0.123 (1.00)	0.598 (1.00)	0.391 (1.00)	0.514 (1.00)
del 11q14 1	25 (28%)	65	0.02 (1.00)	0.00655 (1.00)	0.965 (1.00)	0.551 (1.00)	0.218 (1.00)	0.35 (1.00)	0.281 (1.00)	0.744 (1.00)	0.325 (1.00)	0.582 (1.00)
del 12q14 2	5 (6%)	85	0.0903 (1.00)	0.222 (1.00)			0.178 (1.00)	0.0011 (0.46)	0.595 (1.00)	0.305 (1.00)	0.854 (1.00)	0.15 (1.00)
del 13q14 2	42 (47%)	48	0.00306 (1.00)	0.0889 (1.00)	0.664 (1.00)	0.842 (1.00)	0.334 (1.00)	0.557 (1.00)	1 (1.00)	0.534 (1.00)	0.405 (1.00)	0.827 (1.00)
del 14q21 2	20 (22%)	70	0.0197 (1.00)	0.926 (1.00)	0.655 (1.00)	0.575 (1.00)	0.302 (1.00)	0.284 (1.00)	0.37 (1.00)	0.733 (1.00)	0.27 (1.00)	0.158 (1.00)
del 16p13 3	7 (8%)	83	0.0806 (1.00)	0.557 (1.00)	0.877 (1.00)	0.341 (1.00)	0.545 (1.00)	0.00824 (1.00)	0.0243 (1.00)	0.599 (1.00)	0.02 (1.00)	0.76 (1.00)
del 16q23 1	11 (12%)	79	0.0097 (1.00)	0.507 (1.00)	0.566 (1.00)	0.231 (1.00)	0.0426 (1.00)	0.0108 (1.00)	0.275 (1.00)	0.138 (1.00)	0.0106 (1.00)	0.54 (1.00)
del 17q11 2	24 (27%)	66	0.0149 (1.00)	0.00551 (1.00)	0.643 (1.00)	0.629 (1.00)	0.102 (1.00)	0.105 (1.00)	0.258 (1.00)	0.018 (1.00)	0.111 (1.00)	0.397 (1.00)
del 17q21 31	26 (29%)	64	0.00413 (1.00)	0.00902 (1.00)	0.426 (1.00)	0.541 (1.00)	0.077 (1.00)	0.0461 (1.00)	0.0346 (1.00)	0.00469 (1.00)	0.185 (1.00)	0.0625 (1.00)
del 17q24 2	24 (27%)	66	0.00198 (0.81)	0.0139 (1.00)	0.819 (1.00)	0.289 (1.00)	0.157 (1.00)	0.0404 (1.00)	0.155 (1.00)	0.0269 (1.00)	0.052 (1.00)	0.239 (1.00)
del 18q21 2	36 (40%)	54	0.0307 (1.00)	0.321 (1.00)	1 (1.00)	0.325 (1.00)	0.823 (1.00)	1 (1.00)	0.495 (1.00)	0.914 (1.00)	0.292 (1.00)	0.352 (1.00)
del 20p12 1	12 (13%)	78	0.00514 (1.00)	0.642 (1.00)	0.118 (1.00)	0.619 (1.00)	0.0434 (1.00)	0.0274 (1.00)	0.00654 (1.00)	0.516 (1.00)	0.00183 (0.756)	1 (1.00)
del 22q12 1	50 (56%)	40	0.00486 (1.00)	0.138 (1.00)	0.692 (1.00)	0.292 (1.00)	0.746 (1.00)	0.182 (1.00)	0.635 (1.00)	0.88 (1.00)	0.917 (1.00)	0.2 (1.00)

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.16

Table S1. Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
AMP PEAK 1(1Q22) MUTATED	9	2	0	4	0
AMP PEAK 1(1Q22) WILD-TYPE	9	9	20	14	11

Figure S1. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.083

Table S2. Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 1(1Q22) MUTATED	11	1	2	1
AMP PEAK 1(1Q22) WILD-TYPE	12	22	5	23

Figure S2. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4q35.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S3. Gene #3: 'amp_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 3(4Q35.1) MUTATED	2	10	7	10
AMP PEAK 3(4Q35.1) WILD-TYPE	34	16	9	2

Figure S3. Get High-res Image Gene #3: 'amp_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S4. Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 4(5P15.33) MUTATED	14	25	15	11
AMP PEAK 4(5P15.33) WILD-TYPE	22	1	1	1

Figure S4. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S5. Gene #5: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 5(5Q35.3) MUTATED	12	26	15	10
AMP PEAK 5(5Q35.3) WILD-TYPE	24	0	1	2

Figure S5. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S6. Gene #5: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 5(5Q35.3) MUTATED	7	12	16	20
AMP PEAK 5(5Q35.3) WILD-TYPE	17	1	1	3

Figure S6. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S7. Gene #5: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 5(5Q35.3) MUTATED	8	22	2	23
AMP PEAK 5(5Q35.3) WILD-TYPE	15	1	5	1

Figure S7. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S8. Gene #10: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 10(12Q14.1) MUTATED	19	26	16	9
AMP PEAK 10(12Q14.1) WILD-TYPE	17	0	0	3

Figure S8. Get High-res Image Gene #10: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q11.2' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.044

Table S9. Gene #11: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 11(14Q11.2) MUTATED	7	5	13	2
AMP PEAK 11(14Q11.2) WILD-TYPE	29	21	3	10

Figure S9. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S10. Gene #11: 'amp_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 11(14Q11.2) MUTATED	4	7	11	1
AMP PEAK 11(14Q11.2) WILD-TYPE	20	6	6	22

Figure S10. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S11. Gene #11: 'amp_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 11(14Q11.2) MUTATED	5	16	0	2
AMP PEAK 11(14Q11.2) WILD-TYPE	18	7	7	22

Figure S11. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S12. Gene #11: 'amp_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
AMP PEAK 11(14Q11.2) MUTATED	19	3	2
AMP PEAK 11(14Q11.2) WILD-TYPE	17	13	24

Figure S12. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S13. Gene #12: 'amp_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 12(16P13.3) MUTATED	6	26	11	7
AMP PEAK 12(16P13.3) WILD-TYPE	30	0	5	5

Figure S13. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.074

Table S14. Gene #12: 'amp_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 12(16P13.3) MUTATED	5	9	14	16
AMP PEAK 12(16P13.3) WILD-TYPE	19	4	3	7

Figure S14. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S15. Gene #12: 'amp_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 12(16P13.3) MUTATED	6	19	0	19
AMP PEAK 12(16P13.3) WILD-TYPE	17	4	7	5

Figure S15. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S16. Gene #13: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 13(16Q22.1) MUTATED	10	26	14	6
AMP PEAK 13(16Q22.1) WILD-TYPE	26	0	2	6

Figure S16. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S17. Gene #13: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 13(16Q22.1) MUTATED	9	20	1	18
AMP PEAK 13(16Q22.1) WILD-TYPE	14	3	6	6

Figure S17. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S18. Gene #14: 'amp_16q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 14(16Q24.2) MUTATED	6	26	11	6
AMP PEAK 14(16Q24.2) WILD-TYPE	30	0	5	6

Figure S18. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q24.2' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S19. Gene #14: 'amp_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 14(16Q24.2) MUTATED	5	10	13	16
AMP PEAK 14(16Q24.2) WILD-TYPE	19	3	4	7

Figure S19. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S20. Gene #14: 'amp_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 14(16Q24.2) MUTATED	5	20	1	18
AMP PEAK 14(16Q24.2) WILD-TYPE	18	3	6	6

Figure S20. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.2

Table S21. Gene #16: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 16(19P13.12) MUTATED	16	17	16	9
AMP PEAK 16(19P13.12) WILD-TYPE	20	9	0	3

Figure S21. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.16

Table S22. Gene #16: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 16(19P13.12) MUTATED	15	21	1	12
AMP PEAK 16(19P13.12) WILD-TYPE	8	2	6	12

Figure S22. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.066

Table S23. Gene #18: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 18(XP11.22) MUTATED	11	22	11	5
AMP PEAK 18(XP11.22) WILD-TYPE	25	4	5	7

Figure S23. Get High-res Image Gene #18: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.16

Table S24. Gene #19: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 19(XQ28) MUTATED	10	21	9	6
AMP PEAK 19(XQ28) WILD-TYPE	26	5	7	6

Figure S24. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.049

Table S25. Gene #25: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 6(4Q34.3) MUTATED	4	13	2
DEL PEAK 6(4Q34.3) WILD-TYPE	24	9	25

Figure S25. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.053

Table S26. Gene #26: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 7(4Q34.3) MUTATED	5	15	4
DEL PEAK 7(4Q34.3) WILD-TYPE	23	7	23

Figure S26. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S27. Gene #31: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
DEL PEAK 12(9P23) MUTATED	15	1	4	1
DEL PEAK 12(9P23) WILD-TYPE	9	12	13	22

Figure S27. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S28. Gene #32: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
DEL PEAK 13(9P21.3) MUTATED	17	1	4	2
DEL PEAK 13(9P21.3) WILD-TYPE	7	12	13	21

Figure S28. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S29. Gene #32: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 13(9P21.3) MUTATED	15	4	2	3
DEL PEAK 13(9P21.3) WILD-TYPE	8	19	5	21

Figure S29. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = ACC-TP.transferedmergedcluster.txt
Number of patients = 90
Number of significantly focal cnvs = 46
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