Correlation between copy number variation genes (focal events) and molecular subtypes
Pancreatic Adenocarcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C11G0JRP
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/C11G0JRP
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 40 focal events and 8 molecular subtypes across 81 patients, 59 significant findings detected with P value < 0.05 and Q value < 0.25.

- 3p cnv correlated to 'CN_CNMF'.

- 3q cnv correlated to 'METHLYATION_CNMF'.

- 6p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 6q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 8p cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 8q cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 9p cnv correlated to 'CN_CNMF'.

- 10p cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 10q cnv correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 12p cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 12q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- 16p cnv correlated to 'CN_CNMF'.

- 17p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17q cnv correlated to 'CN_CNMF'.

- 18q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 20p cnv correlated to 'CN_CNMF'.

- 21q cnv correlated to 'CN_CNMF'.

- 22q cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 40 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, 59 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
6q | 35 (43%) | 46 | 5.19e-05 (0.0157) | 1.49e-07 (4.75e-05) | 0.000314 (0.0898) | 4.62e-07 (0.000146) | 7.27e-05 (0.0219) | 8.59e-06 (0.00267) | 1.11e-05 (0.00344) | 4.28e-05 (0.0131)
17p | 34 (42%) | 47 | 7.34e-10 (2.34e-07) | 1.52e-11 (4.87e-09) | 0.000711 (0.194) | 4.46e-05 (0.0135) | 0.000209 (0.0614) | 0.000326 (0.0922) | 1.56e-05 (0.00481) | 0.000123 (0.0365)
8q | 22 (27%) | 59 | 0.00243 (0.578) | 0.000755 (0.204) | 4.42e-05 (0.0135) | 8.83e-05 (0.0265) | 0.000555 (0.154) | 0.000982 (0.255) | 0.000507 (0.142) | 0.000654 (0.18)
12p | 16 (20%) | 65 | 8.07e-06 (0.00253) | 0.00229 (0.551) | 0.000143 (0.0423) | 0.000315 (0.0898) | 0.000263 (0.0761) | 0.0019 (0.47) | 0.000232 (0.0676) | 0.000843 (0.225)
6p | 29 (36%) | 52 | 2.07e-05 (0.00637) | 4.1e-06 (0.00129) | 0.000763 (0.205) | 0.00708 (1.00) | 0.00832 (1.00) | 0.000268 (0.0772) | 0.000315 (0.0898) | 0.00107 (0.275)
8p | 21 (26%) | 60 | 0.00678 (1.00) | 0.000993 (0.256) | 4.42e-05 (0.0135) | 8.83e-05 (0.0265) | 0.000555 (0.154) | 0.000982 (0.255) | 0.000507 (0.142) | 0.000654 (0.18)
10p | 15 (19%) | 66 | 0.000841 (0.225) | 0.0344 (1.00) | 0.019 (1.00) | 0.000786 (0.211) | 0.00192 (0.471) | 0.000862 (0.228) | 0.000212 (0.0619) | 0.000554 (0.154)
10q | 16 (20%) | 65 | 8.07e-06 (0.00253) | 0.0282 (1.00) | 0.0296 (1.00) | 0.00272 (0.634) | 0.00294 (0.677) | 0.0019 (0.47) | 0.000232 (0.0676) | 0.000843 (0.225)
12q | 16 (20%) | 65 | 2.99e-06 (0.000942) | 0.00229 (0.551) | 0.000899 (0.236) | 0.00384 (0.867) | 0.00107 (0.275) | 0.00564 (1.00) | 0.000448 (0.126) | 0.00397 (0.889)
18q | 47 (58%) | 34 | 9.76e-05 (0.0291) | 0.00048 (0.135) | 0.0577 (1.00) | 0.0298 (1.00) | 0.08 (1.00) | 0.0181 (1.00) | 0.00999 (1.00) | 0.0405 (1.00)
3p | 16 (20%) | 65 | 0.000191 (0.0561) | 0.0114 (1.00) | 0.0248 (1.00) | 0.0619 (1.00) | 0.0624 (1.00) | 0.215 (1.00) | 0.0656 (1.00) | 0.141 (1.00)
3q | 15 (19%) | 66 | 0.00428 (0.946) | 0.000936 (0.245) | 0.0121 (1.00) | 0.00942 (1.00) | 0.0421 (1.00) | 0.118 (1.00) | 0.0462 (1.00) | 0.0926 (1.00)
9p | 37 (46%) | 44 | 2.83e-05 (0.00868) | 0.00662 (1.00) | 0.0403 (1.00) | 0.00328 (0.749) | 0.0484 (1.00) | 0.116 (1.00) | 0.04 (1.00) | 0.0766 (1.00)
16p | 10 (12%) | 71 | 0.000738 (0.2) | 0.00247 (0.585) | 0.0244 (1.00) | 0.049 (1.00) | 0.0436 (1.00) | 0.0286 (1.00) | 0.00327 (0.749) | 0.0172 (1.00)
17q | 15 (19%) | 66 | 0.000309 (0.0887) | 0.00177 (0.441) | 0.0121 (1.00) | 0.0214 (1.00) | 0.0421 (1.00) | 0.118 (1.00) | 0.0179 (1.00) | 0.0926 (1.00)
20p | 20 (25%) | 61 | 0.00073 (0.199) | 0.00252 (0.595) | 0.0424 (1.00) | 0.0151 (1.00) | 0.00998 (1.00) | 0.0253 (1.00) | 0.0099 (1.00) | 0.0161 (1.00)
21q | 29 (36%) | 52 | 6.32e-07 (2e-04) | 0.00241 (0.576) | 0.0606 (1.00) | 0.00815 (1.00) | 0.0149 (1.00) | 0.135 (1.00) | 0.043 (1.00) | 0.0816 (1.00)
22q | 20 (25%) | 61 | 0.000177 (0.0523) | 0.0178 (1.00) | 0.0248 (1.00) | 0.0619 (1.00) | 0.124 (1.00) | 0.331 (1.00) | 0.231 (1.00) | 0.256 (1.00)
1p | 17 (21%) | 64 | 0.00797 (1.00) | 0.00209 (0.51) | 0.234 (1.00) | 0.245 (1.00) | 0.306 (1.00) | 0.731 (1.00) | 0.584 (1.00) | 0.668 (1.00)
1q | 22 (27%) | 59 | 0.0685 (1.00) | 0.0121 (1.00) | 0.0602 (1.00) | 0.117 (1.00) | 0.159 (1.00) | 0.614 (1.00) | 0.496 (1.00) | 0.53 (1.00)
2p | 12 (15%) | 69 | 0.00401 (0.894) | 0.0221 (1.00) | 0.26 (1.00) | 0.0209 (1.00) | 0.0772 (1.00) | 0.205 (1.00) | 0.0435 (1.00) | 0.185 (1.00)
2q | 8 (10%) | 73 | 0.0084 (1.00) | 0.00941 (1.00) | 0.00617 (1.00) | 0.00169 (0.422) | 0.0225 (1.00) | 0.138 (1.00) | 0.0383 (1.00) | 0.092 (1.00)
4p | 12 (15%) | 69 | 0.013 (1.00) | 0.112 (1.00) | 0.421 (1.00) | 0.0513 (1.00) | 0.215 (1.00) | 0.561 (1.00) | 0.136 (1.00) | 0.453 (1.00)
4q | 11 (14%) | 70 | 0.0266 (1.00) | 0.0353 (1.00) | 0.349 (1.00) | 0.134 (1.00) | 0.321 (1.00) | 0.38 (1.00) | 0.606 (1.00) | 0.425 (1.00)
5p | 12 (15%) | 69 | 0.00154 (0.389) | 0.0221 (1.00) | 0.0587 (1.00) | 0.0562 (1.00) | 0.108 (1.00) | 0.255 (1.00) | 0.151 (1.00) | 0.195 (1.00)
5q | 12 (15%) | 69 | 0.00154 (0.389) | 0.0221 (1.00) | 0.0587 (1.00) | 0.0562 (1.00) | 0.0436 (1.00) | 0.149 (1.00) | 0.0607 (1.00) | 0.122 (1.00)
7p | 21 (26%) | 60 | 0.0207 (1.00) | 0.00155 (0.39) | 0.0331 (1.00) | 0.0363 (1.00) | 0.0158 (1.00) | 0.174 (1.00) | 0.0383 (1.00) | 0.139 (1.00)
7q | 19 (23%) | 62 | 0.0639 (1.00) | 0.0053 (1.00) | 0.0331 (1.00) | 0.0363 (1.00) | 0.0158 (1.00) | 0.174 (1.00) | 0.0383 (1.00) | 0.139 (1.00)
9q | 24 (30%) | 57 | 0.0848 (1.00) | 0.243 (1.00) | 0.479 (1.00) | 1 (1.00) | 0.482 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
11p | 13 (16%) | 68 | 0.00271 (0.634) | 0.0885 (1.00) | 0.263 (1.00) | 0.777 (1.00) | 0.295 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
11q | 13 (16%) | 68 | 0.0283 (1.00) | 0.175 (1.00) | 0.487 (1.00) | 0.559 (1.00) | 0.816 (1.00) | 0.597 (1.00) | 0.584 (1.00) | 0.608 (1.00)
13q | 16 (20%) | 65 | 0.0293 (1.00) | 1 (1.00) | 0.613 (1.00) | 0.545 (1.00) | 0.434 (1.00) | 0.762 (1.00) | 0.475 (1.00) | 0.641 (1.00)
14q | 13 (16%) | 68 | 0.131 (1.00) | 0.0452 (1.00) | 0.125 (1.00) | 0.196 (1.00) | 0.477 (1.00) | 0.331 (1.00) | 0.49 (1.00) | 0.336 (1.00)
15q | 17 (21%) | 64 | 0.00367 (0.832) | 0.00138 (0.349) | 0.00293 (0.677) | 0.0018 (0.447) | 0.00105 (0.271) | 0.00621 (1.00) | 0.00417 (0.926) | 0.00387 (0.871)
16q | 11 (14%) | 70 | 0.000967 (0.252) | 0.00258 (0.606) | 0.00999 (1.00) | 0.133 (1.00) | 0.0256 (1.00) | 0.00895 (1.00) | 0.00227 (0.549) | 0.0089 (1.00)
18p | 39 (48%) | 42 | 0.131 (1.00) | 0.00509 (1.00) | 0.536 (1.00) | 0.373 (1.00) | 0.438 (1.00) | 0.203 (1.00) | 0.0966 (1.00) | 0.308 (1.00)
19p | 11 (14%) | 70 | 0.0124 (1.00) | 0.197 (1.00) | 0.0296 (1.00) | 0.00272 (0.634) | 0.00844 (1.00) | 0.0291 (1.00) | 0.0118 (1.00) | 0.0253 (1.00)
19q | 14 (17%) | 67 | 0.0976 (1.00) | 0.175 (1.00) | 0.0939 (1.00) | 0.00914 (1.00) | 0.034 (1.00) | 0.0135 (1.00) | 0.037 (1.00) | 0.0921 (1.00)
20q | 18 (22%) | 63 | 0.00223 (0.541) | 0.0349 (1.00) | 0.12 (1.00) | 0.00942 (1.00) | 0.0194 (1.00) | 0.0529 (1.00) | 0.00922 (1.00) | 0.04 (1.00)
xq | 8 (10%) | 73 | 0.134 (1.00) | 0.509 (1.00) | 0.391 (1.00) | 0.615 (1.00) | 0.204 (1.00) | 1 (1.00) | 0.248 (1.00) | 0.342 (1.00)

'3p' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.056

Table S1. Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
3P MUTATED | 3 | 3 | 10
3P WILD-TYPE | 17 | 39 | 9

Figure S1. Get High-res Image Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'METHLYATION_CNMF'

P value = 0.000936 (Fisher's exact test), Q value = 0.25

Table S2. Gene #6: '3q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 34 | 19
3Q MUTATED | 6 | 1 | 8
3Q WILD-TYPE | 21 | 33 | 11

Figure S2. Get High-res Image Gene #6: '3q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p' versus 'CN_CNMF'

P value = 2.07e-05 (Fisher's exact test), Q value = 0.0064

Table S3. Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
6P MUTATED | 9 | 6 | 14
6P WILD-TYPE | 11 | 36 | 5

Figure S3. Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 4.1e-06 (Fisher's exact test), Q value = 0.0013

Table S4. Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 34 | 19
6P MUTATED | 15 | 2 | 11
6P WILD-TYPE | 12 | 32 | 8

Figure S4. Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p' versus 'MRNASEQ_CNMF'

P value = 0.000763 (Fisher's exact test), Q value = 0.21

Table S5. Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 12 | 12 | 10
6P MUTATED | 13 | 2 | 2 | 0
6P WILD-TYPE | 8 | 10 | 10 | 10

Figure S5. Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000268 (Fisher's exact test), Q value = 0.077

Table S6. Gene #11: '6p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 11 | 20 | 27
6P MUTATED | 1 | 2 | 16
6P WILD-TYPE | 10 | 18 | 11

Figure S6. Get High-res Image Gene #11: '6p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000315 (Fisher's exact test), Q value = 0.09

Table S7. Gene #11: '6p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 10 | 23
6P MUTATED | 15 | 0 | 4
6P WILD-TYPE | 10 | 10 | 19

Figure S7. Get High-res Image Gene #11: '6p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q' versus 'CN_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.016

Table S8. Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
6Q MUTATED | 11 | 9 | 15
6Q WILD-TYPE | 9 | 33 | 4

Figure S8. Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'6q' versus 'METHLYATION_CNMF'

P value = 1.49e-07 (Fisher's exact test), Q value = 4.8e-05

Table S9. Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 34 | 19
6Q MUTATED | 20 | 3 | 11
6Q WILD-TYPE | 7 | 31 | 8

Figure S9. Get High-res Image Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'MRNASEQ_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.09

Table S10. Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 12 | 12 | 10
6Q MUTATED | 16 | 2 | 2 | 2
6Q WILD-TYPE | 5 | 10 | 10 | 8

Figure S10. Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.62e-07 (Fisher's exact test), Q value = 0.00015

Table S11. Gene #12: '6q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 22 | 28
6Q MUTATED | 0 | 18 | 4
6Q WILD-TYPE | 5 | 4 | 24

Figure S11. Get High-res Image Gene #12: '6q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_CNMF'

P value = 7.27e-05 (Fisher's exact test), Q value = 0.022

Table S12. Gene #12: '6q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 11 | 18
6Q MUTATED | 20 | 2 | 2
6Q WILD-TYPE | 9 | 9 | 16

Figure S12. Get High-res Image Gene #12: '6q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.59e-06 (Fisher's exact test), Q value = 0.0027

Table S13. Gene #12: '6q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 11 | 20 | 27
6Q MUTATED | 1 | 3 | 20
6Q WILD-TYPE | 10 | 17 | 7

Figure S13. Get High-res Image Gene #12: '6q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0034

Table S14. Gene #12: '6q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 10 | 23
6Q MUTATED | 19 | 1 | 4
6Q WILD-TYPE | 6 | 9 | 19

Figure S14. Get High-res Image Gene #12: '6q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.013

Table S15. Gene #12: '6q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 26 | 20
6Q MUTATED | 2 | 19 | 3
6Q WILD-TYPE | 10 | 7 | 17

Figure S15. Get High-res Image Gene #12: '6q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p' versus 'MRNASEQ_CNMF'

P value = 4.42e-05 (Fisher's exact test), Q value = 0.013

Table S16. Gene #15: '8p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 12 | 12 | 10
8P MUTATED | 13 | 0 | 2 | 0
8P WILD-TYPE | 8 | 12 | 10 | 10

Figure S16. Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.83e-05 (Fisher's exact test), Q value = 0.026

Table S17. Gene #15: '8p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 22 | 28
8P MUTATED | 0 | 13 | 2
8P WILD-TYPE | 5 | 9 | 26

Figure S17. Get High-res Image Gene #15: '8p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_CNMF'

P value = 0.000555 (Fisher's exact test), Q value = 0.15

Table S18. Gene #15: '8p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 11 | 18
8P MUTATED | 15 | 0 | 2
8P WILD-TYPE | 14 | 11 | 16

Figure S18. Get High-res Image Gene #15: '8p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000507 (Fisher's exact test), Q value = 0.14

Table S19. Gene #15: '8p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 10 | 23
8P MUTATED | 14 | 1 | 2
8P WILD-TYPE | 11 | 9 | 21

Figure S19. Get High-res Image Gene #15: '8p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000654 (Fisher's exact test), Q value = 0.18

Table S20. Gene #15: '8p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 26 | 20
8P MUTATED | 2 | 14 | 1
8P WILD-TYPE | 10 | 12 | 19

Figure S20. Get High-res Image Gene #15: '8p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q' versus 'METHLYATION_CNMF'

P value = 0.000755 (Fisher's exact test), Q value = 0.2

Table S21. Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 34 | 19
8Q MUTATED | 12 | 2 | 7
8Q WILD-TYPE | 15 | 32 | 12

Figure S21. Get High-res Image Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q' versus 'MRNASEQ_CNMF'

P value = 4.42e-05 (Fisher's exact test), Q value = 0.013

Table S22. Gene #16: '8q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 12 | 12 | 10
8Q MUTATED | 13 | 0 | 2 | 0
8Q WILD-TYPE | 8 | 12 | 10 | 10

Figure S22. Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.83e-05 (Fisher's exact test), Q value = 0.026

Table S23. Gene #16: '8q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 22 | 28
8Q MUTATED | 0 | 13 | 2
8Q WILD-TYPE | 5 | 9 | 26

Figure S23. Get High-res Image Gene #16: '8q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_CNMF'

P value = 0.000555 (Fisher's exact test), Q value = 0.15

Table S24. Gene #16: '8q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 11 | 18
8Q MUTATED | 15 | 0 | 2
8Q WILD-TYPE | 14 | 11 | 16

Figure S24. Get High-res Image Gene #16: '8q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000507 (Fisher's exact test), Q value = 0.14

Table S25. Gene #16: '8q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 10 | 23
8Q MUTATED | 14 | 1 | 2
8Q WILD-TYPE | 11 | 9 | 21

Figure S25. Get High-res Image Gene #16: '8q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000654 (Fisher's exact test), Q value = 0.18

Table S26. Gene #16: '8q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 26 | 20
8Q MUTATED | 2 | 14 | 1
8Q WILD-TYPE | 10 | 12 | 19

Figure S26. Get High-res Image Gene #16: '8q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p' versus 'CN_CNMF'

P value = 2.83e-05 (Fisher's exact test), Q value = 0.0087

Table S27. Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
9P MUTATED | 11 | 10 | 16
9P WILD-TYPE | 9 | 32 | 3

Figure S27. Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 0.000841 (Fisher's exact test), Q value = 0.22

Table S28. Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
10P MUTATED | 5 | 2 | 8
10P WILD-TYPE | 15 | 40 | 11

Figure S28. Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000786 (Fisher's exact test), Q value = 0.21

Table S29. Gene #19: '10p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 22 | 28
10P MUTATED | 0 | 8 | 0
10P WILD-TYPE | 5 | 14 | 28

Figure S29. Get High-res Image Gene #19: '10p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000862 (Fisher's exact test), Q value = 0.23

Table S30. Gene #19: '10p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 11 | 20 | 27
10P MUTATED | 0 | 0 | 10
10P WILD-TYPE | 11 | 20 | 17

Figure S30. Get High-res Image Gene #19: '10p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.062

Table S31. Gene #19: '10p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 10 | 23
10P MUTATED | 10 | 0 | 0
10P WILD-TYPE | 15 | 10 | 23

Figure S31. Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000554 (Fisher's exact test), Q value = 0.15

Table S32. Gene #19: '10p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 26 | 20
10P MUTATED | 0 | 10 | 0
10P WILD-TYPE | 12 | 16 | 20

Figure S32. Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 8.07e-06 (Fisher's exact test), Q value = 0.0025

Table S33. Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
10Q MUTATED | 5 | 1 | 10
10Q WILD-TYPE | 15 | 41 | 9

Figure S33. Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.068

Table S34. Gene #20: '10q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 10 | 23
10Q MUTATED | 11 | 1 | 0
10Q WILD-TYPE | 14 | 9 | 23

Figure S34. Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000843 (Fisher's exact test), Q value = 0.22

Table S35. Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 26 | 20
10Q MUTATED | 0 | 11 | 1
10Q WILD-TYPE | 12 | 15 | 19

Figure S35. Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p' versus 'CN_CNMF'

P value = 8.07e-06 (Fisher's exact test), Q value = 0.0025

Table S36. Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
12P MUTATED | 5 | 1 | 10
12P WILD-TYPE | 15 | 41 | 9

Figure S36. Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'12p' versus 'MRNASEQ_CNMF'

P value = 0.000143 (Fisher's exact test), Q value = 0.042

Table S37. Gene #23: '12p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 12 | 12 | 10
12P MUTATED | 10 | 0 | 0 | 0
12P WILD-TYPE | 11 | 12 | 12 | 10

Figure S37. Get High-res Image Gene #23: '12p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000315 (Fisher's exact test), Q value = 0.09

Table S38. Gene #23: '12p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 22 | 28
12P MUTATED | 1 | 9 | 0
12P WILD-TYPE | 4 | 13 | 28

Figure S38. Get High-res Image Gene #23: '12p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_CNMF'

P value = 0.000263 (Fisher's exact test), Q value = 0.076

Table S39. Gene #23: '12p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 11 | 18
12P MUTATED | 12 | 0 | 0
12P WILD-TYPE | 17 | 11 | 18

Figure S39. Get High-res Image Gene #23: '12p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'12p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.068

Table S40. Gene #23: '12p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 10 | 23
12P MUTATED | 11 | 1 | 0
12P WILD-TYPE | 14 | 9 | 23

Figure S40. Get High-res Image Gene #23: '12p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000843 (Fisher's exact test), Q value = 0.22

Table S41. Gene #23: '12p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 26 | 20
12P MUTATED | 0 | 11 | 1
12P WILD-TYPE | 12 | 15 | 19

Figure S41. Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 2.99e-06 (Fisher's exact test), Q value = 0.00094

Table S42. Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
12Q MUTATED | 4 | 1 | 11
12Q WILD-TYPE | 16 | 41 | 8

Figure S42. Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

'12q' versus 'MRNASEQ_CNMF'

P value = 0.000899 (Fisher's exact test), Q value = 0.24

Table S43. Gene #24: '12q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 12 | 12 | 10
12Q MUTATED | 10 | 1 | 0 | 0
12Q WILD-TYPE | 11 | 11 | 12 | 10

Figure S43. Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000448 (Fisher's exact test), Q value = 0.13

Table S44. Gene #24: '12q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 10 | 23
12Q MUTATED | 11 | 2 | 0
12Q WILD-TYPE | 14 | 8 | 23

Figure S44. Get High-res Image Gene #24: '12q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p' versus 'CN_CNMF'

P value = 0.000738 (Fisher's exact test), Q value = 0.2

Table S45. Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
16P MUTATED | 2 | 1 | 7
16P WILD-TYPE | 18 | 41 | 12

Figure S45. Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'CN_CNMF'

P value = 7.34e-10 (Fisher's exact test), Q value = 2.3e-07

Table S46. Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
17P MUTATED | 14 | 4 | 16
17P WILD-TYPE | 6 | 38 | 3

Figure S46. Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 1.52e-11 (Fisher's exact test), Q value = 4.9e-09

Table S47. Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 34 | 19
17P MUTATED | 23 | 1 | 10
17P WILD-TYPE | 4 | 33 | 9

Figure S47. Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p' versus 'MRNASEQ_CNMF'

P value = 0.000711 (Fisher's exact test), Q value = 0.19

Table S48. Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 12 | 12 | 10
17P MUTATED | 15 | 3 | 1 | 2
17P WILD-TYPE | 6 | 9 | 11 | 8

Figure S48. Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.46e-05 (Fisher's exact test), Q value = 0.014

Table S49. Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 22 | 28
17P MUTATED | 1 | 16 | 4
17P WILD-TYPE | 4 | 6 | 24

Figure S49. Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.061

Table S50. Gene #30: '17p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 11 | 18
17P MUTATED | 19 | 2 | 2
17P WILD-TYPE | 10 | 9 | 16

Figure S50. Get High-res Image Gene #30: '17p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000326 (Fisher's exact test), Q value = 0.092

Table S51. Gene #30: '17p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 11 | 20 | 27
17P MUTATED | 1 | 4 | 18
17P WILD-TYPE | 10 | 16 | 9

Figure S51. Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0048

Table S52. Gene #30: '17p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 10 | 23
17P MUTATED | 18 | 3 | 2
17P WILD-TYPE | 7 | 7 | 21

Figure S52. Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000123 (Fisher's exact test), Q value = 0.036

Table S53. Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 26 | 20
17P MUTATED | 1 | 18 | 4
17P WILD-TYPE | 11 | 8 | 16

Figure S53. Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.089

Table S54. Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
17Q MUTATED | 4 | 2 | 9
17Q WILD-TYPE | 16 | 40 | 10

Figure S54. Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'CN_CNMF'

P value = 9.76e-05 (Fisher's exact test), Q value = 0.029

Table S55. Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
18Q MUTATED | 19 | 17 | 11
18Q WILD-TYPE | 1 | 25 | 8

Figure S55. Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.13

Table S56. Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 27 | 34 | 19
18Q MUTATED | 21 | 11 | 14
18Q WILD-TYPE | 6 | 23 | 5

Figure S56. Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p' versus 'CN_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.2

Table S57. Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
20P MUTATED | 4 | 5 | 11
20P WILD-TYPE | 16 | 37 | 8

Figure S57. Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

'21q' versus 'CN_CNMF'

P value = 6.32e-07 (Fisher's exact test), Q value = 2e-04

Table S58. Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
21Q MUTATED | 12 | 4 | 13
21Q WILD-TYPE | 8 | 38 | 6

Figure S58. Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'CN_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.052

Table S59. Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 42 | 19
22Q MUTATED | 7 | 3 | 10
22Q WILD-TYPE | 13 | 39 | 9

Figure S59. Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

- Number of patients = 81

- Number of significantly focal cnvs = 40

- 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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