Correlation between copy number variation genes (focal events) and molecular subtypes
Uveal Melanoma (Primary solid tumor)
13 July 2018 | None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
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 21 focal events and 10 molecular subtypes across 80 patients, 131 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_6p24.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- amp_8q11.22 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- amp_8q24.22 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_1p36.12 cnv correlated to 'MRNA_CHIERARCHICAL', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', and 'CN_THRESHOLDED_CNMF'.

- del_1p12 cnv correlated to 'MRNA_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', and 'METHYLATION_CNMF'.

- del_2q37.2 cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- del_3p25.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_3p25.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_3p22.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_3p14.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_3q24 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_3q29 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_3q29 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_6q25.3 cnv correlated to 'LINCRNA_CNMF', 'MIR_MATURE_CNMF', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', and 'METHYLATION_CNMF'.

- del_8p11.22 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_11q24.3 cnv correlated to 'MIR_MATURE_CHIERARCHICAL', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- del_16q22.1 cnv correlated to 'CN_THRESHOLDED_CNMF'.

- del_16q23.3 cnv correlated to 'CN_THRESHOLDED_CNMF'.

- del_17q12 cnv correlated to 'LINCRNA_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 21 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, 131 significant findings detected.

|  | Clinical Features | MRNA CNMF | MRNA CHIERARCHICAL | LINCRNA CNMF | LINCRNA CHIERARCHICAL | MIR MATURE CNMF | MIR MATURE CHIERARCHICAL | CN CNMF | CN THRESHOLDED CNMF | METHYLATION CNMF | METHYLATION 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 6p24 3 | 47 (59%) | 33 | 0.00279 (0.00497) | 2e-05 (4.12e-05) | 0.00061 (0.00112) | 1e-05 (2.14e-05) | 3e-05 (6.06e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 0.00023 (0.000435) | 1e-05 (2.14e-05)
amp 8q11 22 | 48 (60%) | 32 | 8e-05 (0.000157) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 2e-05 (4.12e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05)
amp 8q24 22 | 61 (76%) | 19 | 0.00402 (0.00709) | 0.00108 (0.00197) | 1e-05 (2.14e-05) | 0.00033 (0.000619) | 1e-05 (2.14e-05) | 2e-05 (4.12e-05) | 0.00015 (0.000289) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 8e-05 (0.000157)
del 3p25 2 | 42 (52%) | 38 | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05)
del 3p25 1 | 42 (52%) | 38 | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05)
del 3p22 2 | 42 (52%) | 38 | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05)
del 3p14 2 | 43 (54%) | 37 | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05)
del 3q24 | 44 (55%) | 36 | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05)
del 3q29 | 44 (55%) | 36 | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05)
del 3q29 | 44 (55%) | 36 | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05)
del 8p11 22 | 19 (24%) | 61 | 0.00114 (0.00206) | 9e-05 (0.000175) | 0.00022 (0.00042) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 4e-05 (8e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 3e-05 (6.06e-05)
del 1p12 | 18 (22%) | 62 | 0.0176 (0.0296) | 0.144 (0.214) | 0.354 (0.443) | 0.363 (0.448) | 0.924 (0.929) | 0.0438 (0.0714) | 2e-05 (4.12e-05) | 1e-05 (2.14e-05) | 0.0167 (0.0283) | 0.119 (0.18)
del 6q25 3 | 26 (32%) | 54 | 0.634 (0.7) | 0.147 (0.218) | 0.046 (0.0741) | 0.183 (0.256) | 0.0462 (0.0741) | 0.576 (0.654) | 0.0439 (0.0714) | 1e-05 (2.14e-05) | 0.00203 (0.00364) | 0.222 (0.295)
del 1p36 12 | 25 (31%) | 55 | 0.195 (0.271) | 0.0121 (0.0209) | 0.0514 (0.0818) | 0.0574 (0.0906) | 0.899 (0.921) | 0.0337 (0.0561) | 1e-05 (2.14e-05) | 1e-05 (2.14e-05) | 0.16 (0.231) | 0.227 (0.298)
del 11q24 3 | 7 (9%) | 73 | 0.839 (0.867) | 0.218 (0.291) | 0.0748 (0.116) | 0.16 (0.231) | 0.242 (0.316) | 0.0363 (0.0601) | 0.257 (0.333) | 0.456 (0.544) | 0.00463 (0.0081) | 0.0101 (0.0176)
del 2q37 2 | 4 (5%) | 76 | 0.474 (0.562) | 0.913 (0.922) | 0.263 (0.339) | 0.0135 (0.0231) | 0.661 (0.719) | 0.512 (0.59) | 0.738 (0.784) | 0.93 (0.93) | 0.625 (0.694) | 0.51 (0.59)
del 16q22 1 | 18 (22%) | 62 | 0.216 (0.291) | 0.165 (0.234) | 0.659 (0.719) | 0.433 (0.526) | 0.216 (0.291) | 0.773 (0.816) | 0.317 (0.401) | 1e-05 (2.14e-05) | 0.225 (0.297) | 0.6 (0.678)
del 16q23 3 | 19 (24%) | 61 | 0.158 (0.23) | 0.0883 (0.135) | 0.452 (0.542) | 0.357 (0.444) | 0.114 (0.173) | 0.789 (0.825) | 0.211 (0.289) | 1e-05 (2.14e-05) | 0.124 (0.187) | 0.445 (0.537)
del 17q12 | 3 (4%) | 77 | 0.149 (0.219) | 0.198 (0.274) | 0.00047 (0.000873) | 0.061 (0.0955) | 0.739 (0.784) | 0.218 (0.291) | 0.515 (0.59) | 0.476 (0.562) | 0.0658 (0.102) | 0.173 (0.244)
del 5q23 1 | 4 (5%) | 76 | 0.689 (0.746) | 0.91 (0.922) | 0.398 (0.486) | 0.653 (0.717) | 0.497 (0.583) | 0.612 (0.684) | 0.396 (0.486) | 0.723 (0.779) | 0.162 (0.232) | 0.511 (0.59)
del 18q22 2 | 4 (5%) | 76 | 0.882 (0.908) | 0.521 (0.595) | 0.784 (0.824) | 0.329 (0.414) | 0.801 (0.833) | 0.613 (0.684) | 0.739 (0.784) | 0.298 (0.381) | 0.912 (0.922) | 0.302 (0.385)

'amp_6p24.3' versus 'MRNA_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.005

Table S1. Gene #1: 'amp_6p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
AMP PEAK 1(6P24.3) MUTATED | 4 | 5 | 25 | 10 | 3
AMP PEAK 1(6P24.3) WILD-TYPE | 7 | 6 | 4 | 11 | 5

Figure S1. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.1e-05

Table S2. Gene #1: 'amp_6p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
AMP PEAK 1(6P24.3) MUTATED | 7 | 10 | 25 | 5
AMP PEAK 1(6P24.3) WILD-TYPE | 8 | 5 | 2 | 18

Figure S2. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p24.3' versus 'LINCRNA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0011

Table S3. Gene #1: 'amp_6p24.3' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
AMP PEAK 1(6P24.3) MUTATED | 7 | 3 | 16 | 5 | 16
AMP PEAK 1(6P24.3) WILD-TYPE | 11 | 4 | 12 | 6 | 0

Figure S3. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'amp_6p24.3' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S4. Gene #1: 'amp_6p24.3' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
AMP PEAK 1(6P24.3) MUTATED | 6 | 20 | 6 | 15
AMP PEAK 1(6P24.3) WILD-TYPE | 15 | 4 | 14 | 0

Figure S4. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'amp_6p24.3' versus 'MIR_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.1e-05

Table S5. Gene #1: 'amp_6p24.3' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
AMP PEAK 1(6P24.3) MUTATED | 3 | 9 | 10 | 23 | 2
AMP PEAK 1(6P24.3) WILD-TYPE | 10 | 12 | 8 | 1 | 2

Figure S5. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'amp_6p24.3' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S6. Gene #1: 'amp_6p24.3' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
AMP PEAK 1(6P24.3) MUTATED | 3 | 10 | 5 | 16 | 13
AMP PEAK 1(6P24.3) WILD-TYPE | 18 | 10 | 3 | 1 | 1

Figure S6. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S7. Gene #1: 'amp_6p24.3' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
AMP PEAK 1(6P24.3) MUTATED | 5 | 9 | 33 | 0 | 0
AMP PEAK 1(6P24.3) WILD-TYPE | 13 | 12 | 4 | 2 | 2

Figure S7. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #7: 'CN_CNMF'

'amp_6p24.3' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S8. Gene #1: 'amp_6p24.3' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
AMP PEAK 1(6P24.3) MUTATED | 4 | 3 | 18 | 12 | 2 | 2 | 4 | 2
AMP PEAK 1(6P24.3) WILD-TYPE | 12 | 4 | 4 | 0 | 0 | 12 | 1 | 0

Figure S8. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'amp_6p24.3' versus 'METHYLATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00044

Table S9. Gene #1: 'amp_6p24.3' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
AMP PEAK 1(6P24.3) MUTATED | 10 | 9 | 7 | 21
AMP PEAK 1(6P24.3) WILD-TYPE | 18 | 4 | 9 | 2

Figure S9. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'amp_6p24.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S10. Gene #1: 'amp_6p24.3' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
AMP PEAK 1(6P24.3) MUTATED | 12 | 11 | 24
AMP PEAK 1(6P24.3) WILD-TYPE | 28 | 4 | 1

Figure S10. Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'amp_8q11.22' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S11. Gene #2: 'amp_8q11.22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
AMP PEAK 2(8Q11.22) MUTATED | 10 | 8 | 8 | 14 | 8
AMP PEAK 2(8Q11.22) WILD-TYPE | 1 | 3 | 21 | 7 | 0

Figure S11. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q11.22' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S12. Gene #2: 'amp_8q11.22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
AMP PEAK 2(8Q11.22) MUTATED | 15 | 7 | 6 | 20
AMP PEAK 2(8Q11.22) WILD-TYPE | 0 | 8 | 21 | 3

Figure S12. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q11.22' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S13. Gene #2: 'amp_8q11.22' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
AMP PEAK 2(8Q11.22) MUTATED | 18 | 0 | 18 | 5 | 7
AMP PEAK 2(8Q11.22) WILD-TYPE | 0 | 7 | 10 | 6 | 9

Figure S13. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'amp_8q11.22' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S14. Gene #2: 'amp_8q11.22' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
AMP PEAK 2(8Q11.22) MUTATED | 19 | 5 | 18 | 6
AMP PEAK 2(8Q11.22) WILD-TYPE | 2 | 19 | 2 | 9

Figure S14. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'amp_8q11.22' versus 'MIR_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.1e-05

Table S15. Gene #2: 'amp_8q11.22' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
AMP PEAK 2(8Q11.22) MUTATED | 12 | 19 | 4 | 11 | 2
AMP PEAK 2(8Q11.22) WILD-TYPE | 1 | 2 | 14 | 13 | 2

Figure S15. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'amp_8q11.22' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S16. Gene #2: 'amp_8q11.22' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
AMP PEAK 2(8Q11.22) MUTATED | 20 | 17 | 1 | 6 | 4
AMP PEAK 2(8Q11.22) WILD-TYPE | 1 | 3 | 7 | 11 | 10

Figure S16. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'amp_8q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S17. Gene #2: 'amp_8q11.22' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
AMP PEAK 2(8Q11.22) MUTATED | 15 | 21 | 10 | 1 | 1
AMP PEAK 2(8Q11.22) WILD-TYPE | 3 | 0 | 27 | 1 | 1

Figure S17. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #7: 'CN_CNMF'

'amp_8q11.22' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S18. Gene #2: 'amp_8q11.22' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
AMP PEAK 2(8Q11.22) MUTATED | 13 | 7 | 4 | 4 | 2 | 12 | 5 | 1
AMP PEAK 2(8Q11.22) WILD-TYPE | 3 | 0 | 18 | 8 | 0 | 2 | 0 | 1

Figure S18. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'amp_8q11.22' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S19. Gene #2: 'amp_8q11.22' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
AMP PEAK 2(8Q11.22) MUTATED | 28 | 2 | 10 | 8
AMP PEAK 2(8Q11.22) WILD-TYPE | 0 | 11 | 6 | 15

Figure S19. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'amp_8q11.22' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S20. Gene #2: 'amp_8q11.22' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
AMP PEAK 2(8Q11.22) MUTATED | 36 | 4 | 8
AMP PEAK 2(8Q11.22) WILD-TYPE | 4 | 11 | 17

Figure S20. Get High-res Image Gene #2: 'amp_8q11.22' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'amp_8q24.22' versus 'MRNA_CNMF'

P value = 0.00402 (Fisher's exact test), Q value = 0.0071

Table S21. Gene #3: 'amp_8q24.22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
AMP PEAK 3(8Q24.22) MUTATED | 10 | 9 | 15 | 19 | 8
AMP PEAK 3(8Q24.22) WILD-TYPE | 1 | 2 | 14 | 2 | 0

Figure S21. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.22' versus 'MRNA_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.002

Table S22. Gene #3: 'amp_8q24.22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
AMP PEAK 3(8Q24.22) MUTATED | 15 | 10 | 15 | 21
AMP PEAK 3(8Q24.22) WILD-TYPE | 0 | 5 | 12 | 2

Figure S22. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.22' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S23. Gene #3: 'amp_8q24.22' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
AMP PEAK 3(8Q24.22) MUTATED | 18 | 0 | 25 | 6 | 12
AMP PEAK 3(8Q24.22) WILD-TYPE | 0 | 7 | 3 | 5 | 4

Figure S23. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'amp_8q24.22' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00062

Table S24. Gene #3: 'amp_8q24.22' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
AMP PEAK 3(8Q24.22) MUTATED | 20 | 13 | 19 | 9
AMP PEAK 3(8Q24.22) WILD-TYPE | 1 | 11 | 1 | 6

Figure S24. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'amp_8q24.22' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S25. Gene #3: 'amp_8q24.22' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
AMP PEAK 3(8Q24.22) MUTATED | 12 | 21 | 7 | 19 | 2
AMP PEAK 3(8Q24.22) WILD-TYPE | 1 | 0 | 11 | 5 | 2

Figure S25. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'amp_8q24.22' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.1e-05

Table S26. Gene #3: 'amp_8q24.22' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
AMP PEAK 3(8Q24.22) MUTATED | 20 | 20 | 1 | 11 | 9
AMP PEAK 3(8Q24.22) WILD-TYPE | 1 | 0 | 7 | 6 | 5

Figure S26. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S27. Gene #3: 'amp_8q24.22' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
AMP PEAK 3(8Q24.22) MUTATED | 16 | 21 | 20 | 2 | 2
AMP PEAK 3(8Q24.22) WILD-TYPE | 2 | 0 | 17 | 0 | 0

Figure S27. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #7: 'CN_CNMF'

'amp_8q24.22' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S28. Gene #3: 'amp_8q24.22' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
AMP PEAK 3(8Q24.22) MUTATED | 15 | 7 | 5 | 12 | 2 | 13 | 5 | 2
AMP PEAK 3(8Q24.22) WILD-TYPE | 1 | 0 | 17 | 0 | 0 | 1 | 0 | 0

Figure S28. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'amp_8q24.22' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S29. Gene #3: 'amp_8q24.22' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
AMP PEAK 3(8Q24.22) MUTATED | 28 | 3 | 13 | 17
AMP PEAK 3(8Q24.22) WILD-TYPE | 0 | 10 | 3 | 6

Figure S29. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'amp_8q24.22' versus 'METHYLATION_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S30. Gene #3: 'amp_8q24.22' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
AMP PEAK 3(8Q24.22) MUTATED | 38 | 6 | 17
AMP PEAK 3(8Q24.22) WILD-TYPE | 2 | 9 | 8

Figure S30. Get High-res Image Gene #3: 'amp_8q24.22' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_1p36.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.021

Table S31. Gene #4: 'del_1p36.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
DEL PEAK 1(1P36.12) MUTATED | 3 | 5 | 4 | 13
DEL PEAK 1(1P36.12) WILD-TYPE | 12 | 10 | 23 | 10

Figure S31. Get High-res Image Gene #4: 'del_1p36.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.12' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.056

Table S32. Gene #4: 'del_1p36.12' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 1(1P36.12) MUTATED | 12 | 4 | 1 | 6 | 2
DEL PEAK 1(1P36.12) WILD-TYPE | 9 | 16 | 7 | 11 | 12

Figure S32. Get High-res Image Gene #4: 'del_1p36.12' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_1p36.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S33. Gene #4: 'del_1p36.12' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 1(1P36.12) MUTATED | 16 | 2 | 6 | 0 | 1
DEL PEAK 1(1P36.12) WILD-TYPE | 2 | 19 | 31 | 2 | 1

Figure S33. Get High-res Image Gene #4: 'del_1p36.12' versus Molecular Subtype #7: 'CN_CNMF'

'del_1p36.12' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S34. Gene #4: 'del_1p36.12' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 1(1P36.12) MUTATED | 16 | 1 | 2 | 1 | 2 | 0 | 1 | 2
DEL PEAK 1(1P36.12) WILD-TYPE | 0 | 6 | 20 | 11 | 0 | 14 | 4 | 0

Figure S34. Get High-res Image Gene #4: 'del_1p36.12' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_1p12' versus 'MRNA_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.03

Table S35. Gene #5: 'del_1p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
DEL PEAK 2(1P12) MUTATED | 6 | 3 | 3 | 6 | 0
DEL PEAK 2(1P12) WILD-TYPE | 5 | 8 | 26 | 15 | 8

Figure S35. Get High-res Image Gene #5: 'del_1p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p12' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.071

Table S36. Gene #5: 'del_1p12' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 2(1P12) MUTATED | 9 | 3 | 0 | 5 | 1
DEL PEAK 2(1P12) WILD-TYPE | 12 | 17 | 8 | 12 | 13

Figure S36. Get High-res Image Gene #5: 'del_1p12' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_1p12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.1e-05

Table S37. Gene #5: 'del_1p12' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 2(1P12) MUTATED | 12 | 2 | 4 | 0 | 0
DEL PEAK 2(1P12) WILD-TYPE | 6 | 19 | 33 | 2 | 2

Figure S37. Get High-res Image Gene #5: 'del_1p12' versus Molecular Subtype #7: 'CN_CNMF'

'del_1p12' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S38. Gene #5: 'del_1p12' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 2(1P12) MUTATED | 12 | 0 | 2 | 0 | 0 | 0 | 2 | 2
DEL PEAK 2(1P12) WILD-TYPE | 4 | 7 | 20 | 12 | 2 | 14 | 3 | 0

Figure S38. Get High-res Image Gene #5: 'del_1p12' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_1p12' versus 'METHYLATION_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.028

Table S39. Gene #5: 'del_1p12' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 2(1P12) MUTATED | 8 | 0 | 7 | 3
DEL PEAK 2(1P12) WILD-TYPE | 20 | 13 | 9 | 20

Figure S39. Get High-res Image Gene #5: 'del_1p12' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_2q37.2' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.023

Table S40. Gene #6: 'del_2q37.2' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
DEL PEAK 3(2Q37.2) MUTATED | 0 | 0 | 1 | 3
DEL PEAK 3(2Q37.2) WILD-TYPE | 21 | 24 | 19 | 12

Figure S40. Get High-res Image Gene #6: 'del_2q37.2' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'del_3p25.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S41. Gene #7: 'del_3p25.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
DEL PEAK 4(3P25.2) MUTATED | 11 | 7 | 1 | 15 | 8
DEL PEAK 4(3P25.2) WILD-TYPE | 0 | 4 | 28 | 6 | 0

Figure S41. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p25.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S42. Gene #7: 'del_3p25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
DEL PEAK 4(3P25.2) MUTATED | 15 | 3 | 1 | 23
DEL PEAK 4(3P25.2) WILD-TYPE | 0 | 12 | 26 | 0

Figure S42. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p25.2' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S43. Gene #7: 'del_3p25.2' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 4(3P25.2) MUTATED | 18 | 0 | 17 | 6 | 1
DEL PEAK 4(3P25.2) WILD-TYPE | 0 | 7 | 11 | 5 | 15

Figure S43. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'del_3p25.2' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S44. Gene #7: 'del_3p25.2' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
DEL PEAK 4(3P25.2) MUTATED | 20 | 1 | 20 | 1
DEL PEAK 4(3P25.2) WILD-TYPE | 1 | 23 | 0 | 14

Figure S44. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'del_3p25.2' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S45. Gene #7: 'del_3p25.2' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
DEL PEAK 4(3P25.2) MUTATED | 11 | 20 | 6 | 3 | 2
DEL PEAK 4(3P25.2) WILD-TYPE | 2 | 1 | 12 | 21 | 2

Figure S45. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'del_3p25.2' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S46. Gene #7: 'del_3p25.2' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 4(3P25.2) MUTATED | 21 | 17 | 0 | 2 | 2
DEL PEAK 4(3P25.2) WILD-TYPE | 0 | 3 | 8 | 15 | 12

Figure S46. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_3p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S47. Gene #7: 'del_3p25.2' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 4(3P25.2) MUTATED | 17 | 21 | 1 | 2 | 1
DEL PEAK 4(3P25.2) WILD-TYPE | 1 | 0 | 36 | 0 | 1

Figure S47. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #7: 'CN_CNMF'

'del_3p25.2' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S48. Gene #7: 'del_3p25.2' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 4(3P25.2) MUTATED | 15 | 7 | 0 | 0 | 1 | 14 | 5 | 0
DEL PEAK 4(3P25.2) WILD-TYPE | 1 | 0 | 22 | 12 | 1 | 0 | 0 | 2

Figure S48. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_3p25.2' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S49. Gene #7: 'del_3p25.2' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 4(3P25.2) MUTATED | 28 | 1 | 11 | 2
DEL PEAK 4(3P25.2) WILD-TYPE | 0 | 12 | 5 | 21

Figure S49. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_3p25.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S50. Gene #7: 'del_3p25.2' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
DEL PEAK 4(3P25.2) MUTATED | 40 | 0 | 2
DEL PEAK 4(3P25.2) WILD-TYPE | 0 | 15 | 23

Figure S50. Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_3p25.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S51. Gene #8: 'del_3p25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
DEL PEAK 5(3P25.1) MUTATED | 11 | 7 | 1 | 15 | 8
DEL PEAK 5(3P25.1) WILD-TYPE | 0 | 4 | 28 | 6 | 0

Figure S51. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p25.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S52. Gene #8: 'del_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
DEL PEAK 5(3P25.1) MUTATED | 15 | 3 | 1 | 23
DEL PEAK 5(3P25.1) WILD-TYPE | 0 | 12 | 26 | 0

Figure S52. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p25.1' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S53. Gene #8: 'del_3p25.1' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 5(3P25.1) MUTATED | 18 | 0 | 17 | 6 | 1
DEL PEAK 5(3P25.1) WILD-TYPE | 0 | 7 | 11 | 5 | 15

Figure S53. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'del_3p25.1' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S54. Gene #8: 'del_3p25.1' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
DEL PEAK 5(3P25.1) MUTATED | 20 | 1 | 20 | 1
DEL PEAK 5(3P25.1) WILD-TYPE | 1 | 23 | 0 | 14

Figure S54. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'del_3p25.1' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S55. Gene #8: 'del_3p25.1' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
DEL PEAK 5(3P25.1) MUTATED | 11 | 20 | 6 | 3 | 2
DEL PEAK 5(3P25.1) WILD-TYPE | 2 | 1 | 12 | 21 | 2

Figure S55. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'del_3p25.1' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S56. Gene #8: 'del_3p25.1' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 5(3P25.1) MUTATED | 21 | 17 | 0 | 2 | 2
DEL PEAK 5(3P25.1) WILD-TYPE | 0 | 3 | 8 | 15 | 12

Figure S56. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S57. Gene #8: 'del_3p25.1' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 5(3P25.1) MUTATED | 17 | 21 | 1 | 2 | 1
DEL PEAK 5(3P25.1) WILD-TYPE | 1 | 0 | 36 | 0 | 1

Figure S57. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #7: 'CN_CNMF'

'del_3p25.1' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S58. Gene #8: 'del_3p25.1' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 5(3P25.1) MUTATED | 15 | 7 | 0 | 0 | 1 | 14 | 5 | 0
DEL PEAK 5(3P25.1) WILD-TYPE | 1 | 0 | 22 | 12 | 1 | 0 | 0 | 2

Figure S58. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_3p25.1' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S59. Gene #8: 'del_3p25.1' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 5(3P25.1) MUTATED | 28 | 1 | 11 | 2
DEL PEAK 5(3P25.1) WILD-TYPE | 0 | 12 | 5 | 21

Figure S59. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_3p25.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S60. Gene #8: 'del_3p25.1' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
DEL PEAK 5(3P25.1) MUTATED | 40 | 0 | 2
DEL PEAK 5(3P25.1) WILD-TYPE | 0 | 15 | 23

Figure S60. Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_3p22.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S61. Gene #9: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
DEL PEAK 6(3P22.2) MUTATED | 11 | 7 | 1 | 15 | 8
DEL PEAK 6(3P22.2) WILD-TYPE | 0 | 4 | 28 | 6 | 0

Figure S61. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p22.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S62. Gene #9: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
DEL PEAK 6(3P22.2) MUTATED | 15 | 3 | 1 | 23
DEL PEAK 6(3P22.2) WILD-TYPE | 0 | 12 | 26 | 0

Figure S62. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p22.2' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S63. Gene #9: 'del_3p22.2' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 6(3P22.2) MUTATED | 18 | 0 | 17 | 6 | 1
DEL PEAK 6(3P22.2) WILD-TYPE | 0 | 7 | 11 | 5 | 15

Figure S63. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'del_3p22.2' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S64. Gene #9: 'del_3p22.2' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
DEL PEAK 6(3P22.2) MUTATED | 20 | 1 | 20 | 1
DEL PEAK 6(3P22.2) WILD-TYPE | 1 | 23 | 0 | 14

Figure S64. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'del_3p22.2' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S65. Gene #9: 'del_3p22.2' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
DEL PEAK 6(3P22.2) MUTATED | 11 | 20 | 6 | 3 | 2
DEL PEAK 6(3P22.2) WILD-TYPE | 2 | 1 | 12 | 21 | 2

Figure S65. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'del_3p22.2' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S66. Gene #9: 'del_3p22.2' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 6(3P22.2) MUTATED | 21 | 17 | 0 | 2 | 2
DEL PEAK 6(3P22.2) WILD-TYPE | 0 | 3 | 8 | 15 | 12

Figure S66. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S67. Gene #9: 'del_3p22.2' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 6(3P22.2) MUTATED | 17 | 21 | 1 | 2 | 1
DEL PEAK 6(3P22.2) WILD-TYPE | 1 | 0 | 36 | 0 | 1

Figure S67. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #7: 'CN_CNMF'

'del_3p22.2' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S68. Gene #9: 'del_3p22.2' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 6(3P22.2) MUTATED | 15 | 7 | 0 | 0 | 1 | 14 | 5 | 0
DEL PEAK 6(3P22.2) WILD-TYPE | 1 | 0 | 22 | 12 | 1 | 0 | 0 | 2

Figure S68. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_3p22.2' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S69. Gene #9: 'del_3p22.2' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 6(3P22.2) MUTATED | 28 | 1 | 11 | 2
DEL PEAK 6(3P22.2) WILD-TYPE | 0 | 12 | 5 | 21

Figure S69. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_3p22.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S70. Gene #9: 'del_3p22.2' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
DEL PEAK 6(3P22.2) MUTATED | 40 | 0 | 2
DEL PEAK 6(3P22.2) WILD-TYPE | 0 | 15 | 23

Figure S70. Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_3p14.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S71. Gene #10: 'del_3p14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
DEL PEAK 7(3P14.2) MUTATED | 11 | 7 | 2 | 15 | 8
DEL PEAK 7(3P14.2) WILD-TYPE | 0 | 4 | 27 | 6 | 0

Figure S71. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p14.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S72. Gene #10: 'del_3p14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
DEL PEAK 7(3P14.2) MUTATED | 15 | 4 | 1 | 23
DEL PEAK 7(3P14.2) WILD-TYPE | 0 | 11 | 26 | 0

Figure S72. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p14.2' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S73. Gene #10: 'del_3p14.2' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 7(3P14.2) MUTATED | 18 | 0 | 17 | 7 | 1
DEL PEAK 7(3P14.2) WILD-TYPE | 0 | 7 | 11 | 4 | 15

Figure S73. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'del_3p14.2' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S74. Gene #10: 'del_3p14.2' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
DEL PEAK 7(3P14.2) MUTATED | 21 | 1 | 20 | 1
DEL PEAK 7(3P14.2) WILD-TYPE | 0 | 23 | 0 | 14

Figure S74. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'del_3p14.2' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S75. Gene #10: 'del_3p14.2' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
DEL PEAK 7(3P14.2) MUTATED | 11 | 21 | 6 | 3 | 2
DEL PEAK 7(3P14.2) WILD-TYPE | 2 | 0 | 12 | 21 | 2

Figure S75. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'del_3p14.2' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S76. Gene #10: 'del_3p14.2' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 7(3P14.2) MUTATED | 21 | 18 | 0 | 2 | 2
DEL PEAK 7(3P14.2) WILD-TYPE | 0 | 2 | 8 | 15 | 12

Figure S76. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S77. Gene #10: 'del_3p14.2' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 7(3P14.2) MUTATED | 17 | 21 | 1 | 2 | 2
DEL PEAK 7(3P14.2) WILD-TYPE | 1 | 0 | 36 | 0 | 0

Figure S77. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #7: 'CN_CNMF'

'del_3p14.2' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S78. Gene #10: 'del_3p14.2' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 7(3P14.2) MUTATED | 16 | 7 | 0 | 0 | 1 | 14 | 5 | 0
DEL PEAK 7(3P14.2) WILD-TYPE | 0 | 0 | 22 | 12 | 1 | 0 | 0 | 2

Figure S78. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_3p14.2' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S79. Gene #10: 'del_3p14.2' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 7(3P14.2) MUTATED | 28 | 2 | 11 | 2
DEL PEAK 7(3P14.2) WILD-TYPE | 0 | 11 | 5 | 21

Figure S79. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_3p14.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S80. Gene #10: 'del_3p14.2' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
DEL PEAK 7(3P14.2) MUTATED | 40 | 1 | 2
DEL PEAK 7(3P14.2) WILD-TYPE | 0 | 14 | 23

Figure S80. Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_3q24' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S81. Gene #11: 'del_3q24' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
DEL PEAK 8(3Q24) MUTATED | 11 | 7 | 3 | 15 | 8
DEL PEAK 8(3Q24) WILD-TYPE | 0 | 4 | 26 | 6 | 0

Figure S81. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3q24' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S82. Gene #11: 'del_3q24' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
DEL PEAK 8(3Q24) MUTATED | 15 | 4 | 2 | 23
DEL PEAK 8(3Q24) WILD-TYPE | 0 | 11 | 25 | 0

Figure S82. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3q24' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S83. Gene #11: 'del_3q24' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 8(3Q24) MUTATED | 18 | 0 | 17 | 7 | 2
DEL PEAK 8(3Q24) WILD-TYPE | 0 | 7 | 11 | 4 | 14

Figure S83. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'del_3q24' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S84. Gene #11: 'del_3q24' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
DEL PEAK 8(3Q24) MUTATED | 21 | 1 | 20 | 2
DEL PEAK 8(3Q24) WILD-TYPE | 0 | 23 | 0 | 13

Figure S84. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'del_3q24' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S85. Gene #11: 'del_3q24' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
DEL PEAK 8(3Q24) MUTATED | 11 | 21 | 7 | 3 | 2
DEL PEAK 8(3Q24) WILD-TYPE | 2 | 0 | 11 | 21 | 2

Figure S85. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'del_3q24' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S86. Gene #11: 'del_3q24' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 8(3Q24) MUTATED | 21 | 18 | 1 | 2 | 2
DEL PEAK 8(3Q24) WILD-TYPE | 0 | 2 | 7 | 15 | 12

Figure S86. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_3q24' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S87. Gene #11: 'del_3q24' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 8(3Q24) MUTATED | 17 | 21 | 2 | 2 | 2
DEL PEAK 8(3Q24) WILD-TYPE | 1 | 0 | 35 | 0 | 0

Figure S87. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #7: 'CN_CNMF'

'del_3q24' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S88. Gene #11: 'del_3q24' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 8(3Q24) MUTATED | 16 | 7 | 0 | 0 | 2 | 14 | 5 | 0
DEL PEAK 8(3Q24) WILD-TYPE | 0 | 0 | 22 | 12 | 0 | 0 | 0 | 2

Figure S88. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_3q24' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S89. Gene #11: 'del_3q24' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 8(3Q24) MUTATED | 28 | 3 | 11 | 2
DEL PEAK 8(3Q24) WILD-TYPE | 0 | 10 | 5 | 21

Figure S89. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_3q24' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S90. Gene #11: 'del_3q24' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
DEL PEAK 8(3Q24) MUTATED | 40 | 2 | 2
DEL PEAK 8(3Q24) WILD-TYPE | 0 | 13 | 23

Figure S90. Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_3q29' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S91. Gene #12: 'del_3q29' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
DEL PEAK 9(3Q29) MUTATED | 11 | 7 | 3 | 15 | 8
DEL PEAK 9(3Q29) WILD-TYPE | 0 | 4 | 26 | 6 | 0

Figure S91. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3q29' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S92. Gene #12: 'del_3q29' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
DEL PEAK 9(3Q29) MUTATED | 15 | 4 | 2 | 23
DEL PEAK 9(3Q29) WILD-TYPE | 0 | 11 | 25 | 0

Figure S92. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3q29' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S93. Gene #12: 'del_3q29' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 9(3Q29) MUTATED | 18 | 0 | 17 | 7 | 2
DEL PEAK 9(3Q29) WILD-TYPE | 0 | 7 | 11 | 4 | 14

Figure S93. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'del_3q29' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S94. Gene #12: 'del_3q29' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
DEL PEAK 9(3Q29) MUTATED | 21 | 1 | 20 | 2
DEL PEAK 9(3Q29) WILD-TYPE | 0 | 23 | 0 | 13

Figure S94. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'del_3q29' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S95. Gene #12: 'del_3q29' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
DEL PEAK 9(3Q29) MUTATED | 11 | 21 | 7 | 3 | 2
DEL PEAK 9(3Q29) WILD-TYPE | 2 | 0 | 11 | 21 | 2

Figure S95. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'del_3q29' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S96. Gene #12: 'del_3q29' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 9(3Q29) MUTATED | 21 | 18 | 1 | 2 | 2
DEL PEAK 9(3Q29) WILD-TYPE | 0 | 2 | 7 | 15 | 12

Figure S96. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S97. Gene #12: 'del_3q29' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 9(3Q29) MUTATED | 17 | 21 | 2 | 2 | 2
DEL PEAK 9(3Q29) WILD-TYPE | 1 | 0 | 35 | 0 | 0

Figure S97. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #7: 'CN_CNMF'

'del_3q29' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S98. Gene #12: 'del_3q29' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 9(3Q29) MUTATED | 16 | 7 | 0 | 0 | 2 | 14 | 5 | 0
DEL PEAK 9(3Q29) WILD-TYPE | 0 | 0 | 22 | 12 | 0 | 0 | 0 | 2

Figure S98. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_3q29' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S99. Gene #12: 'del_3q29' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 9(3Q29) MUTATED | 28 | 3 | 11 | 2
DEL PEAK 9(3Q29) WILD-TYPE | 0 | 10 | 5 | 21

Figure S99. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_3q29' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S100. Gene #12: 'del_3q29' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
DEL PEAK 9(3Q29) MUTATED | 40 | 2 | 2
DEL PEAK 9(3Q29) WILD-TYPE | 0 | 13 | 23

Figure S100. Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_3q29' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S101. Gene #13: 'del_3q29' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
DEL PEAK 10(3Q29) MUTATED | 11 | 7 | 3 | 15 | 8
DEL PEAK 10(3Q29) WILD-TYPE | 0 | 4 | 26 | 6 | 0

Figure S101. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3q29' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S102. Gene #13: 'del_3q29' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
DEL PEAK 10(3Q29) MUTATED | 15 | 4 | 2 | 23
DEL PEAK 10(3Q29) WILD-TYPE | 0 | 11 | 25 | 0

Figure S102. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3q29' versus 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S103. Gene #13: 'del_3q29' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 10(3Q29) MUTATED | 18 | 0 | 17 | 7 | 2
DEL PEAK 10(3Q29) WILD-TYPE | 0 | 7 | 11 | 4 | 14

Figure S103. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'del_3q29' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S104. Gene #13: 'del_3q29' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
DEL PEAK 10(3Q29) MUTATED | 21 | 1 | 20 | 2
DEL PEAK 10(3Q29) WILD-TYPE | 0 | 23 | 0 | 13

Figure S104. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'del_3q29' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S105. Gene #13: 'del_3q29' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
DEL PEAK 10(3Q29) MUTATED | 11 | 21 | 7 | 3 | 2
DEL PEAK 10(3Q29) WILD-TYPE | 2 | 0 | 11 | 21 | 2

Figure S105. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'del_3q29' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S106. Gene #13: 'del_3q29' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 10(3Q29) MUTATED | 21 | 18 | 1 | 2 | 2
DEL PEAK 10(3Q29) WILD-TYPE | 0 | 2 | 7 | 15 | 12

Figure S106. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S107. Gene #13: 'del_3q29' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 10(3Q29) MUTATED | 17 | 21 | 2 | 2 | 2
DEL PEAK 10(3Q29) WILD-TYPE | 1 | 0 | 35 | 0 | 0

Figure S107. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #7: 'CN_CNMF'

'del_3q29' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S108. Gene #13: 'del_3q29' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 10(3Q29) MUTATED | 16 | 7 | 0 | 0 | 2 | 14 | 5 | 0
DEL PEAK 10(3Q29) WILD-TYPE | 0 | 0 | 22 | 12 | 0 | 0 | 0 | 2

Figure S108. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_3q29' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S109. Gene #13: 'del_3q29' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 10(3Q29) MUTATED | 28 | 3 | 11 | 2
DEL PEAK 10(3Q29) WILD-TYPE | 0 | 10 | 5 | 21

Figure S109. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_3q29' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S110. Gene #13: 'del_3q29' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
DEL PEAK 10(3Q29) MUTATED | 40 | 2 | 2
DEL PEAK 10(3Q29) WILD-TYPE | 0 | 13 | 23

Figure S110. Get High-res Image Gene #13: 'del_3q29' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_6q25.3' versus 'LINCRNA_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.074

Table S111. Gene #15: 'del_6q25.3' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 12(6Q25.3) MUTATED | 8 | 0 | 9 | 1 | 8
DEL PEAK 12(6Q25.3) WILD-TYPE | 10 | 7 | 19 | 10 | 8

Figure S111. Get High-res Image Gene #15: 'del_6q25.3' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'del_6q25.3' versus 'MIR_MATURE_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.074

Table S112. Gene #15: 'del_6q25.3' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
DEL PEAK 12(6Q25.3) MUTATED | 5 | 11 | 2 | 8 | 0
DEL PEAK 12(6Q25.3) WILD-TYPE | 8 | 10 | 16 | 16 | 4

Figure S112. Get High-res Image Gene #15: 'del_6q25.3' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'del_6q25.3' versus 'CN_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.071

Table S113. Gene #15: 'del_6q25.3' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 12(6Q25.3) MUTATED | 3 | 12 | 11 | 0 | 0
DEL PEAK 12(6Q25.3) WILD-TYPE | 15 | 9 | 26 | 2 | 2

Figure S113. Get High-res Image Gene #15: 'del_6q25.3' versus Molecular Subtype #7: 'CN_CNMF'

'del_6q25.3' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S114. Gene #15: 'del_6q25.3' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 12(6Q25.3) MUTATED | 2 | 7 | 0 | 8 | 2 | 0 | 5 | 2
DEL PEAK 12(6Q25.3) WILD-TYPE | 14 | 0 | 22 | 4 | 0 | 14 | 0 | 0

Figure S114. Get High-res Image Gene #15: 'del_6q25.3' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_6q25.3' versus 'METHYLATION_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.0036

Table S115. Gene #15: 'del_6q25.3' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 12(6Q25.3) MUTATED | 14 | 1 | 1 | 10
DEL PEAK 12(6Q25.3) WILD-TYPE | 14 | 12 | 15 | 13

Figure S115. Get High-res Image Gene #15: 'del_6q25.3' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_8p11.22' versus 'MRNA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0021

Table S116. Gene #16: 'del_8p11.22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
DEL PEAK 13(8P11.22) MUTATED | 5 | 3 | 1 | 5 | 5
DEL PEAK 13(8P11.22) WILD-TYPE | 6 | 8 | 28 | 16 | 3

Figure S116. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p11.22' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00017

Table S117. Gene #16: 'del_8p11.22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
DEL PEAK 13(8P11.22) MUTATED | 10 | 2 | 1 | 6
DEL PEAK 13(8P11.22) WILD-TYPE | 5 | 13 | 26 | 17

Figure S117. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p11.22' versus 'LINCRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00042

Table S118. Gene #16: 'del_8p11.22' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 13(8P11.22) MUTATED | 12 | 0 | 5 | 1 | 1
DEL PEAK 13(8P11.22) WILD-TYPE | 6 | 7 | 23 | 10 | 15

Figure S118. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'del_8p11.22' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S119. Gene #16: 'del_8p11.22' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
DEL PEAK 13(8P11.22) MUTATED | 13 | 0 | 5 | 1
DEL PEAK 13(8P11.22) WILD-TYPE | 8 | 24 | 15 | 14

Figure S119. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'del_8p11.22' versus 'MIR_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S120. Gene #16: 'del_8p11.22' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
DEL PEAK 13(8P11.22) MUTATED | 6 | 12 | 0 | 0 | 1
DEL PEAK 13(8P11.22) WILD-TYPE | 7 | 9 | 18 | 24 | 3

Figure S120. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'del_8p11.22' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8e-05

Table S121. Gene #16: 'del_8p11.22' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 13(8P11.22) MUTATED | 10 | 9 | 0 | 0 | 0
DEL PEAK 13(8P11.22) WILD-TYPE | 11 | 11 | 8 | 17 | 14

Figure S121. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_8p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S122. Gene #16: 'del_8p11.22' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
DEL PEAK 13(8P11.22) MUTATED | 0 | 17 | 1 | 0 | 1
DEL PEAK 13(8P11.22) WILD-TYPE | 18 | 4 | 36 | 2 | 1

Figure S122. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #7: 'CN_CNMF'

'del_8p11.22' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S123. Gene #16: 'del_8p11.22' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 13(8P11.22) MUTATED | 0 | 7 | 0 | 1 | 0 | 7 | 4 | 0
DEL PEAK 13(8P11.22) WILD-TYPE | 16 | 0 | 22 | 11 | 2 | 7 | 1 | 2

Figure S123. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_8p11.22' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S124. Gene #16: 'del_8p11.22' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 13(8P11.22) MUTATED | 16 | 1 | 1 | 1
DEL PEAK 13(8P11.22) WILD-TYPE | 12 | 12 | 15 | 22

Figure S124. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_8p11.22' versus 'METHYLATION_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.1e-05

Table S125. Gene #16: 'del_8p11.22' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
DEL PEAK 13(8P11.22) MUTATED | 18 | 0 | 1
DEL PEAK 13(8P11.22) WILD-TYPE | 22 | 15 | 24

Figure S125. Get High-res Image Gene #16: 'del_8p11.22' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_11q24.3' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.06

Table S126. Gene #17: 'del_11q24.3' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
DEL PEAK 14(11Q24.3) MUTATED | 0 | 1 | 0 | 2 | 4
DEL PEAK 14(11Q24.3) WILD-TYPE | 21 | 19 | 8 | 15 | 10

Figure S126. Get High-res Image Gene #17: 'del_11q24.3' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'del_11q24.3' versus 'METHYLATION_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.0081

Table S127. Gene #17: 'del_11q24.3' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
DEL PEAK 14(11Q24.3) MUTATED | 0 | 0 | 1 | 6
DEL PEAK 14(11Q24.3) WILD-TYPE | 28 | 13 | 15 | 17

Figure S127. Get High-res Image Gene #17: 'del_11q24.3' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'del_11q24.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.018

Table S128. Gene #17: 'del_11q24.3' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
DEL PEAK 14(11Q24.3) MUTATED | 1 | 0 | 6
DEL PEAK 14(11Q24.3) WILD-TYPE | 39 | 15 | 19

Figure S128. Get High-res Image Gene #17: 'del_11q24.3' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'del_16q22.1' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S129. Gene #18: 'del_16q22.1' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 15(16Q22.1) MUTATED | 3 | 7 | 1 | 2 | 2 | 1 | 0 | 2
DEL PEAK 15(16Q22.1) WILD-TYPE | 13 | 0 | 21 | 10 | 0 | 13 | 5 | 0

Figure S129. Get High-res Image Gene #18: 'del_16q22.1' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_16q23.3' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S130. Gene #19: 'del_16q23.3' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
DEL PEAK 16(16Q23.3) MUTATED | 3 | 7 | 1 | 2 | 2 | 1 | 1 | 2
DEL PEAK 16(16Q23.3) WILD-TYPE | 13 | 0 | 21 | 10 | 0 | 13 | 4 | 0

Figure S130. Get High-res Image Gene #19: 'del_16q23.3' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'del_17q12' versus 'LINCRNA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.00087

Table S131. Gene #20: 'del_17q12' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
DEL PEAK 17(17Q12) MUTATED | 0 | 3 | 0 | 0 | 0
DEL PEAK 17(17Q12) WILD-TYPE | 18 | 4 | 28 | 11 | 16

Figure S131. Get High-res Image Gene #20: 'del_17q12' versus Molecular Subtype #3: 'LINCRNA_CNMF'

Methods & Data
Input

- Copy number data file = all_lesions.txt from GISTIC pipeline

- Processed Copy number data file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/b4064356-ee8a-4343-8cf6-a53725085a29/correlate_genomic_events_all/cdb097d1-98f2-4c0d-994f-520683eda8fc/call-preprocess_genomic_event/transformed.cor.cli.txt

- Molecular subtype file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/9d897bdb-7a9a-423a-ad17-06f28ae98803/aggregate_clusters_workflow/1d8bac82-5a1d-4cd2-aeb1-8ddd0e1e7a20/call-aggregate_clusters/TCGA-UVM-TP.transposedmergedcluster.txt

- Number of patients = 80

- Number of significantly focal cnvs = 21

- 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.

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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