Correlation between copy number variation genes (focal events) and molecular subtypes
Testicular Germ Cell Tumors (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C19K496N
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/C19K496N
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 47 focal events and 8 molecular subtypes across 150 patients, 42 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_7q11.22 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- amp_8q11.23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_8q23.3 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- amp_16q21 cnv correlated to 'CN_CNMF'.

- amp_22q11.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_6p22.3 cnv correlated to 'CN_CNMF'.

- del_6q26 cnv correlated to 'METHLYATION_CNMF'.

- del_9q33.3 cnv correlated to 'CN_CNMF'.

- del_9q34.2 cnv correlated to 'CN_CNMF'.

- del_10p15.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- del_10q23.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_11p15.5 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- del_11q12.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_11q24.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_19q13.41 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_xp21.1 cnv correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 47 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 42 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
del 19q13 41 | 58 (39%) | 92 | 1e-05 (0.00364) | 1e-05 (0.00364) | 1e-05 (0.00364) | 1e-05 (0.00364) | 1e-05 (0.00364) | 1e-05 (0.00364) | 1e-05 (0.00364) | 1e-05 (0.00364)
del 11q12 3 | 114 (76%) | 36 | 1e-05 (0.00364) | 0.186 (1.00) | 7e-05 (0.024) | 1e-05 (0.00364) | 3e-05 (0.0104) | 0.00029 (0.0969) | 0.00748 (1.00) | 0.00728 (1.00)
del 10q26 3 | 76 (51%) | 74 | 0.00047 (0.154) | 1e-05 (0.00364) | 1e-05 (0.00364) | 0.00015 (0.0507) | 0.588 (1.00) | 0.0347 (1.00) | 0.0384 (1.00) | 0.0111 (1.00)
amp 8q11 23 | 122 (81%) | 28 | 4e-05 (0.0139) | 0.00966 (1.00) | 1e-05 (0.00364) | 4e-05 (0.0139) | 0.0126 (1.00) | 0.0261 (1.00) | 0.0239 (1.00) | 0.0829 (1.00)
amp 22q11 21 | 57 (38%) | 93 | 1e-05 (0.00364) | 0.00719 (1.00) | 0.00013 (0.0441) | 1e-05 (0.00364) | 0.0702 (1.00) | 0.236 (1.00) | 0.331 (1.00) | 0.0443 (1.00)
del 10q23 1 | 71 (47%) | 79 | 0.00596 (1.00) | 1e-05 (0.00364) | 4e-05 (0.0139) | 0.00022 (0.0737) | 0.357 (1.00) | 0.0487 (1.00) | 0.0834 (1.00) | 0.0363 (1.00)
amp 7q11 22 | 120 (80%) | 30 | 0.0006 (0.196) | 0.0393 (1.00) | 5e-05 (0.0172) | 0.00229 (0.701) | 0.0159 (1.00) | 0.00368 (1.00) | 0.0153 (1.00) | 0.0467 (1.00)
amp 8q23 3 | 108 (72%) | 42 | 0.184 (1.00) | 0.00328 (0.977) | 0.00035 (0.116) | 0.00058 (0.19) | 0.00603 (1.00) | 0.0208 (1.00) | 0.0354 (1.00) | 0.143 (1.00)
del 10p15 3 | 84 (56%) | 66 | 0.00124 (0.391) | 0.00036 (0.119) | 0.0002 (0.0674) | 0.00113 (0.359) | 0.9 (1.00) | 0.0596 (1.00) | 0.234 (1.00) | 0.279 (1.00)
del 11p15 5 | 94 (63%) | 56 | 0.0251 (1.00) | 0.256 (1.00) | 0.003 (0.9) | 0.00402 (1.00) | 0.0002 (0.0674) | 0.00037 (0.122) | 0.00125 (0.392) | 0.0163 (1.00)
del 11q24 2 | 122 (81%) | 28 | 7e-05 (0.024) | 0.725 (1.00) | 0.00897 (1.00) | 0.00068 (0.22) | 0.00094 (0.301) | 0.0379 (1.00) | 0.019 (1.00) | 0.0431 (1.00)
amp 16q21 | 21 (14%) | 129 | 8e-05 (0.0272) | 0.373 (1.00) | 0.00282 (0.854) | 0.0076 (1.00) | 0.0346 (1.00) | 0.00285 (0.861) | 0.0011 (0.351) | 0.0407 (1.00)
del 6p22 3 | 24 (16%) | 126 | 7e-05 (0.024) | 0.0157 (1.00) | 0.00386 (1.00) | 0.0126 (1.00) | 0.322 (1.00) | 0.0777 (1.00) | 0.116 (1.00) | 0.224 (1.00)
del 6q26 | 26 (17%) | 124 | 0.0324 (1.00) | 0.00075 (0.242) | 0.00592 (1.00) | 0.00135 (0.421) | 0.468 (1.00) | 0.29 (1.00) | 0.246 (1.00) | 0.459 (1.00)
del 9q33 3 | 60 (40%) | 90 | 0.00037 (0.122) | 0.394 (1.00) | 0.118 (1.00) | 0.0156 (1.00) | 0.32 (1.00) | 0.00252 (0.769) | 0.0262 (1.00) | 0.0538 (1.00)
del 9q34 2 | 60 (40%) | 90 | 0.00029 (0.0969) | 0.276 (1.00) | 0.0954 (1.00) | 0.00396 (1.00) | 0.509 (1.00) | 0.0125 (1.00) | 0.0754 (1.00) | 0.182 (1.00)
del xp21 1 | 28 (19%) | 122 | 0.0585 (1.00) | 0.00067 (0.218) | 0.0453 (1.00) | 0.0523 (1.00) | 0.357 (1.00) | 0.245 (1.00) | 0.082 (1.00) | 0.158 (1.00)
amp 1q21 2 | 69 (46%) | 81 | 0.0778 (1.00) | 0.718 (1.00) | 0.87 (1.00) | 0.00085 (0.274) | 0.0178 (1.00) | 0.445 (1.00) | 0.673 (1.00) | 0.194 (1.00)
amp 2p24 1 | 62 (41%) | 88 | 0.00407 (1.00) | 0.00087 (0.279) | 0.0191 (1.00) | 0.0441 (1.00) | 0.188 (1.00) | 0.19 (1.00) | 0.202 (1.00) | 0.316 (1.00)
amp 3q27 3 | 49 (33%) | 101 | 0.0776 (1.00) | 0.102 (1.00) | 0.00254 (0.772) | 0.00771 (1.00) | 0.152 (1.00) | 0.183 (1.00) | 0.259 (1.00) | 0.233 (1.00)
amp 4q12 | 20 (13%) | 130 | 0.00849 (1.00) | 0.661 (1.00) | 0.393 (1.00) | 0.394 (1.00) | 0.863 (1.00) | 0.69 (1.00) | 0.129 (1.00) | 0.429 (1.00)
amp 7p22 1 | 126 (84%) | 24 | 0.0863 (1.00) | 0.0779 (1.00) | 0.0289 (1.00) | 0.103 (1.00) | 0.042 (1.00) | 0.0362 (1.00) | 0.191 (1.00) | 0.177 (1.00)
amp 12p13 33 | 145 (97%) | 5 | 0.053 (1.00) | 0.102 (1.00) | 0.0826 (1.00) | 0.684 (1.00) |  |  |  |
amp 12p12 1 | 147 (98%) | 3 | 0.0549 (1.00) | 0.109 (1.00) | 0.444 (1.00) | 0.558 (1.00) |  |  |  |
amp 12p11 21 | 144 (96%) | 6 | 0.108 (1.00) | 0.0391 (1.00) | 0.036 (1.00) | 0.497 (1.00) | 0.11 (1.00) | 0.469 (1.00) | 0.188 (1.00) | 0.236 (1.00)
amp 12q15 | 100 (67%) | 50 | 0.527 (1.00) | 0.93 (1.00) | 0.813 (1.00) | 0.734 (1.00) | 0.325 (1.00) | 0.564 (1.00) | 0.837 (1.00) | 0.628 (1.00)
amp 20q11 21 | 51 (34%) | 99 | 0.0048 (1.00) | 0.00292 (0.879) | 0.00301 (0.9) | 0.0342 (1.00) | 0.0121 (1.00) | 0.0487 (1.00) | 0.0304 (1.00) | 0.0279 (1.00)
del 1p36 31 | 34 (23%) | 116 | 0.282 (1.00) | 0.733 (1.00) | 0.00228 (0.7) | 0.0507 (1.00) | 0.115 (1.00) | 0.0778 (1.00) | 0.127 (1.00) | 0.33 (1.00)
del 1p31 1 | 27 (18%) | 123 | 0.00709 (1.00) | 0.601 (1.00) | 0.247 (1.00) | 0.723 (1.00) | 0.396 (1.00) | 0.42 (1.00) | 0.498 (1.00) | 0.866 (1.00)
del 1q42 12 | 9 (6%) | 141 | 0.0386 (1.00) | 0.52 (1.00) | 0.562 (1.00) | 0.195 (1.00) | 0.133 (1.00) | 0.188 (1.00) | 0.114 (1.00) | 0.0605 (1.00)
del 2q37 3 | 15 (10%) | 135 | 0.457 (1.00) | 0.0408 (1.00) | 0.0576 (1.00) | 0.173 (1.00) | 0.676 (1.00) | 0.0283 (1.00) | 0.117 (1.00) | 0.215 (1.00)
del 3p26 2 | 41 (27%) | 109 | 0.76 (1.00) | 0.0207 (1.00) | 0.00133 (0.416) | 0.00382 (1.00) | 0.0497 (1.00) | 0.0743 (1.00) | 0.0907 (1.00) | 0.0391 (1.00)
del 4q22 2 | 110 (73%) | 40 | 0.0211 (1.00) | 0.0321 (1.00) | 0.00897 (1.00) | 0.00144 (0.448) | 0.116 (1.00) | 0.108 (1.00) | 0.624 (1.00) | 0.506 (1.00)
del 5p15 2 | 101 (67%) | 49 | 0.187 (1.00) | 0.489 (1.00) | 0.214 (1.00) | 0.457 (1.00) | 0.685 (1.00) | 0.222 (1.00) | 0.34 (1.00) | 0.368 (1.00)
del 5p14 3 | 103 (69%) | 47 | 0.264 (1.00) | 0.318 (1.00) | 0.18 (1.00) | 0.294 (1.00) | 0.528 (1.00) | 0.123 (1.00) | 0.237 (1.00) | 0.304 (1.00)
del 5q12 1 | 105 (70%) | 45 | 0.0895 (1.00) | 0.104 (1.00) | 0.0302 (1.00) | 0.00745 (1.00) | 0.501 (1.00) | 0.0489 (1.00) | 0.1 (1.00) | 0.155 (1.00)
del 7q11 22 | 4 (3%) | 146 | 0.315 (1.00) | 0.00722 (1.00) | 0.00916 (1.00) | 0.0301 (1.00) |  |  |  |
del 7q36 1 | 15 (10%) | 135 | 0.0509 (1.00) | 0.889 (1.00) | 0.201 (1.00) | 0.00989 (1.00) | 0.455 (1.00) | 0.724 (1.00) | 0.0837 (1.00) | 0.18 (1.00)
del 9p24 3 | 70 (47%) | 80 | 0.0909 (1.00) | 0.896 (1.00) | 1 (1.00) | 0.805 (1.00) | 0.284 (1.00) | 0.768 (1.00) | 0.32 (1.00) | 0.374 (1.00)
del 9p23 | 66 (44%) | 84 | 0.0383 (1.00) | 0.915 (1.00) | 0.908 (1.00) | 0.523 (1.00) | 0.325 (1.00) | 0.804 (1.00) | 0.293 (1.00) | 0.41 (1.00)
del 11p12 | 99 (66%) | 51 | 0.0556 (1.00) | 0.111 (1.00) | 0.00163 (0.504) | 0.00523 (1.00) | 0.00338 (1.00) | 0.00373 (1.00) | 0.0296 (1.00) | 0.0483 (1.00)
del 13q34 | 113 (75%) | 37 | 0.0441 (1.00) | 0.554 (1.00) | 0.0828 (1.00) | 0.00191 (0.588) | 0.418 (1.00) | 0.276 (1.00) | 0.00349 (1.00) | 0.0274 (1.00)
del 16q23 1 | 66 (44%) | 84 | 0.00118 (0.373) | 0.234 (1.00) | 0.357 (1.00) | 0.393 (1.00) | 0.292 (1.00) | 0.437 (1.00) | 0.162 (1.00) | 0.251 (1.00)
del 18p11 32 | 118 (79%) | 32 | 0.699 (1.00) | 0.132 (1.00) | 0.0503 (1.00) | 0.247 (1.00) | 0.124 (1.00) | 0.098 (1.00) | 0.0844 (1.00) | 0.108 (1.00)
del 18q22 2 | 125 (83%) | 25 | 0.0586 (1.00) | 0.143 (1.00) | 0.109 (1.00) | 0.133 (1.00) | 0.155 (1.00) | 0.2 (1.00) | 0.0207 (1.00) | 0.00596 (1.00)
del 20p12 1 | 29 (19%) | 121 | 0.335 (1.00) | 0.336 (1.00) | 0.31 (1.00) | 0.095 (1.00) | 0.492 (1.00) | 0.187 (1.00) | 0.111 (1.00) | 0.0741 (1.00)
del xq27 3 | 30 (20%) | 120 | 0.00113 (0.359) | 0.00157 (0.487) | 0.0942 (1.00) | 0.0627 (1.00) | 0.591 (1.00) | 0.383 (1.00) | 0.101 (1.00) | 0.604 (1.00)

'amp_7q11.22' versus 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.2

Table S1. Gene #6: 'amp_7q11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
AMP PEAK 6(7Q11.22) MUTATED | 35 | 43 | 42
AMP PEAK 6(7Q11.22) WILD-TYPE | 13 | 1 | 16

Figure S1. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q11.22' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.017

Table S2. Gene #6: 'amp_7q11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
AMP PEAK 6(7Q11.22) MUTATED | 63 | 35 | 22
AMP PEAK 6(7Q11.22) WILD-TYPE | 7 | 5 | 18

Figure S2. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q11.23' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S3. Gene #7: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
AMP PEAK 7(8Q11.23) MUTATED | 35 | 44 | 43
AMP PEAK 7(8Q11.23) WILD-TYPE | 13 | 0 | 15

Figure S3. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S4. Gene #7: 'amp_8q11.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
AMP PEAK 7(8Q11.23) MUTATED | 67 | 31 | 24
AMP PEAK 7(8Q11.23) WILD-TYPE | 3 | 9 | 16

Figure S4. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S5. Gene #7: 'amp_8q11.23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
AMP PEAK 7(8Q11.23) MUTATED | 40 | 27 | 8 | 18 | 6 | 19 | 4
AMP PEAK 7(8Q11.23) WILD-TYPE | 3 | 0 | 4 | 6 | 2 | 4 | 9

Figure S5. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.12

Table S6. Gene #8: 'amp_8q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
AMP PEAK 8(8Q23.3) MUTATED | 60 | 28 | 20
AMP PEAK 8(8Q23.3) WILD-TYPE | 10 | 12 | 20

Figure S6. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.19

Table S7. Gene #8: 'amp_8q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
AMP PEAK 8(8Q23.3) MUTATED | 38 | 22 | 9 | 15 | 5 | 16 | 3
AMP PEAK 8(8Q23.3) WILD-TYPE | 5 | 5 | 3 | 9 | 3 | 7 | 10

Figure S7. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_16q21' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.027

Table S8. Gene #13: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
AMP PEAK 13(16Q21) MUTATED | 2 | 2 | 17
AMP PEAK 13(16Q21) WILD-TYPE | 46 | 42 | 41

Figure S8. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S9. Gene #15: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
AMP PEAK 15(22Q11.21) MUTATED | 13 | 30 | 14
AMP PEAK 15(22Q11.21) WILD-TYPE | 35 | 14 | 44

Figure S9. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.044

Table S10. Gene #15: 'amp_22q11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
AMP PEAK 15(22Q11.21) MUTATED | 39 | 10 | 8
AMP PEAK 15(22Q11.21) WILD-TYPE | 31 | 30 | 32

Figure S10. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S11. Gene #15: 'amp_22q11.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
AMP PEAK 15(22Q11.21) MUTATED | 16 | 23 | 4 | 5 | 1 | 5 | 3
AMP PEAK 15(22Q11.21) WILD-TYPE | 27 | 4 | 8 | 19 | 7 | 18 | 10

Figure S11. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6p22.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.024

Table S12. Gene #25: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
DEL PEAK 10(6P22.3) MUTATED | 2 | 3 | 19
DEL PEAK 10(6P22.3) WILD-TYPE | 46 | 41 | 39

Figure S12. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.24

Table S13. Gene #26: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
DEL PEAK 11(6Q26) MUTATED | 2 | 14 | 10
DEL PEAK 11(6Q26) WILD-TYPE | 54 | 35 | 35

Figure S13. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q33.3' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.12

Table S14. Gene #31: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
DEL PEAK 16(9Q33.3) MUTATED | 12 | 13 | 35
DEL PEAK 16(9Q33.3) WILD-TYPE | 36 | 31 | 23

Figure S14. Get High-res Image Gene #31: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.2' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.097

Table S15. Gene #32: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
DEL PEAK 17(9Q34.2) MUTATED | 12 | 13 | 35
DEL PEAK 17(9Q34.2) WILD-TYPE | 36 | 31 | 23

Figure S15. Get High-res Image Gene #32: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.12

Table S16. Gene #33: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
DEL PEAK 18(10P15.3) MUTATED | 21 | 37 | 26
DEL PEAK 18(10P15.3) WILD-TYPE | 35 | 12 | 19

Figure S16. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.067

Table S17. Gene #33: 'del_10p15.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
DEL PEAK 18(10P15.3) MUTATED | 28 | 32 | 24
DEL PEAK 18(10P15.3) WILD-TYPE | 42 | 8 | 16

Figure S17. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S18. Gene #34: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
DEL PEAK 19(10Q23.1) MUTATED | 15 | 37 | 19
DEL PEAK 19(10Q23.1) WILD-TYPE | 41 | 12 | 26

Figure S18. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S19. Gene #34: 'del_10q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
DEL PEAK 19(10Q23.1) MUTATED | 22 | 31 | 18
DEL PEAK 19(10Q23.1) WILD-TYPE | 48 | 9 | 22

Figure S19. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.074

Table S20. Gene #34: 'del_10q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
DEL PEAK 19(10Q23.1) MUTATED | 14 | 8 | 9 | 12 | 5 | 19 | 4
DEL PEAK 19(10Q23.1) WILD-TYPE | 29 | 19 | 3 | 12 | 3 | 4 | 9

Figure S20. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.15

Table S21. Gene #35: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
DEL PEAK 20(10Q26.3) MUTATED | 18 | 17 | 41
DEL PEAK 20(10Q26.3) WILD-TYPE | 30 | 27 | 17

Figure S21. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S22. Gene #35: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
DEL PEAK 20(10Q26.3) MUTATED | 16 | 38 | 22
DEL PEAK 20(10Q26.3) WILD-TYPE | 40 | 11 | 23

Figure S22. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S23. Gene #35: 'del_10q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
DEL PEAK 20(10Q26.3) MUTATED | 24 | 33 | 19
DEL PEAK 20(10Q26.3) WILD-TYPE | 46 | 7 | 21

Figure S23. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.051

Table S24. Gene #35: 'del_10q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
DEL PEAK 20(10Q26.3) MUTATED | 16 | 8 | 10 | 13 | 6 | 19 | 4
DEL PEAK 20(10Q26.3) WILD-TYPE | 27 | 19 | 2 | 11 | 2 | 4 | 9

Figure S24. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.067

Table S25. Gene #36: 'del_11p15.5' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 21 | 16 | 25
DEL PEAK 21(11P15.5) MUTATED | 10 | 15 | 4 | 22
DEL PEAK 21(11P15.5) WILD-TYPE | 2 | 6 | 12 | 3

Figure S25. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.12

Table S26. Gene #36: 'del_11p15.5' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 15 | 15
DEL PEAK 21(11P15.5) MUTATED | 36 | 11 | 4
DEL PEAK 21(11P15.5) WILD-TYPE | 8 | 4 | 11

Figure S26. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S27. Gene #38: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
DEL PEAK 23(11Q12.3) MUTATED | 30 | 43 | 41
DEL PEAK 23(11Q12.3) WILD-TYPE | 18 | 1 | 17

Figure S27. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q12.3' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.024

Table S28. Gene #38: 'del_11q12.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
DEL PEAK 23(11Q12.3) MUTATED | 62 | 32 | 20
DEL PEAK 23(11Q12.3) WILD-TYPE | 8 | 8 | 20

Figure S28. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S29. Gene #38: 'del_11q12.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
DEL PEAK 23(11Q12.3) MUTATED | 35 | 27 | 9 | 14 | 6 | 20 | 3
DEL PEAK 23(11Q12.3) WILD-TYPE | 8 | 0 | 3 | 10 | 2 | 3 | 10

Figure S29. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11q12.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.01

Table S30. Gene #38: 'del_11q12.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 21 | 16 | 25
DEL PEAK 23(11Q12.3) MUTATED | 9 | 20 | 6 | 24
DEL PEAK 23(11Q12.3) WILD-TYPE | 3 | 1 | 10 | 1

Figure S30. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.097

Table S31. Gene #38: 'del_11q12.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 15 | 15
DEL PEAK 23(11Q12.3) MUTATED | 39 | 14 | 6
DEL PEAK 23(11Q12.3) WILD-TYPE | 5 | 1 | 9

Figure S31. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11q24.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.024

Table S32. Gene #39: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
DEL PEAK 24(11Q24.2) MUTATED | 33 | 44 | 45
DEL PEAK 24(11Q24.2) WILD-TYPE | 15 | 0 | 13

Figure S32. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.22

Table S33. Gene #39: 'del_11q24.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
DEL PEAK 24(11Q24.2) MUTATED | 35 | 27 | 10 | 18 | 7 | 20 | 5
DEL PEAK 24(11Q24.2) WILD-TYPE | 8 | 0 | 2 | 6 | 1 | 3 | 8

Figure S33. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S34. Gene #44: 'del_19q13.41' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 48 | 44 | 58
DEL PEAK 29(19Q13.41) MUTATED | 14 | 7 | 37
DEL PEAK 29(19Q13.41) WILD-TYPE | 34 | 37 | 21

Figure S34. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.41' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S35. Gene #44: 'del_19q13.41' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
DEL PEAK 29(19Q13.41) MUTATED | 2 | 37 | 19
DEL PEAK 29(19Q13.41) WILD-TYPE | 54 | 12 | 26

Figure S35. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.41' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S36. Gene #44: 'del_19q13.41' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 40 | 40
DEL PEAK 29(19Q13.41) MUTATED | 1 | 33 | 24
DEL PEAK 29(19Q13.41) WILD-TYPE | 69 | 7 | 16

Figure S36. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19q13.41' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S37. Gene #44: 'del_19q13.41' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 43 | 27 | 12 | 24 | 8 | 23 | 13
DEL PEAK 29(19Q13.41) MUTATED | 0 | 1 | 11 | 14 | 5 | 20 | 7
DEL PEAK 29(19Q13.41) WILD-TYPE | 43 | 26 | 1 | 10 | 3 | 3 | 6

Figure S37. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S38. Gene #44: 'del_19q13.41' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 21 | 16 | 25
DEL PEAK 29(19Q13.41) MUTATED | 0 | 15 | 8 | 1
DEL PEAK 29(19Q13.41) WILD-TYPE | 12 | 6 | 8 | 24

Figure S38. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_19q13.41' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S39. Gene #44: 'del_19q13.41' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 15 | 15
DEL PEAK 29(19Q13.41) MUTATED | 2 | 14 | 8
DEL PEAK 29(19Q13.41) WILD-TYPE | 42 | 1 | 7

Figure S39. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S40. Gene #44: 'del_19q13.41' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 22 | 13 | 20 | 19
DEL PEAK 29(19Q13.41) MUTATED | 1 | 11 | 0 | 12
DEL PEAK 29(19Q13.41) WILD-TYPE | 21 | 2 | 20 | 7

Figure S40. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_19q13.41' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S41. Gene #44: 'del_19q13.41' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 8 | 15 | 11 | 5 | 13 | 11
DEL PEAK 29(19Q13.41) MUTATED | 0 | 0 | 14 | 6 | 3 | 1 | 0
DEL PEAK 29(19Q13.41) WILD-TYPE | 11 | 8 | 1 | 5 | 2 | 12 | 11

Figure S41. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.22

Table S42. Gene #46: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 49 | 45
DEL PEAK 31(XP21.1) MUTATED | 5 | 6 | 17
DEL PEAK 31(XP21.1) WILD-TYPE | 51 | 43 | 28

Figure S42. Get High-res Image Gene #46: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

- Molecular subtype file = TGCT-TP.transferedmergedcluster.txt

- Number of patients = 150

- Number of significantly focal cnvs = 47

- Number of molecular subtypes = 8

- Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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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