Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
17 April 2019 | None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 95 arm-level events and 2 molecular subtypes across 110 patients, 54 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 2p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 2q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 5q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 7p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 7q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 10q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- 12p gain cnv correlated to 'MRNA_CHIERARCHICAL'.

- 16p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 16q gain cnv correlated to 'MRNA_CHIERARCHICAL'.

- 18p gain cnv correlated to 'MRNA_CHIERARCHICAL'.

- 18q gain cnv correlated to 'MRNA_CHIERARCHICAL'.

- 20p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 21q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- xp gain cnv correlated to 'MRNA_CHIERARCHICAL'.

- 1p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 3p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 3q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 5q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 10q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 11p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 12p loss cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- 12q loss cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- 15q loss cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- 16p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 18p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 18q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 21p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 21q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- 22p loss cnv correlated to 'MRNA_CHIERARCHICAL'.

- 22q loss cnv correlated to 'MRNA_CHIERARCHICAL'.

- yp loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- yq loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 95 arm-level events and 2 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 54 significant findings detected.

|  | Clinical Features | MRNA CHIERARCHICAL | LINCRNA CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test
1p gain | 32 (29%) | 78 | 0.0229 (0.124) | 0.0286 (0.139)
2p gain | 23 (21%) | 87 | 0.00555 (0.0662) | 0.0186 (0.114)
2q gain | 21 (19%) | 89 | 0.0167 (0.11) | 0.0353 (0.156)
5q gain | 26 (24%) | 84 | 0.0156 (0.11) | 0.00038 (0.0361)
7p gain | 58 (53%) | 52 | 0.0301 (0.139) | 0.00974 (0.0839)
7q gain | 48 (44%) | 62 | 0.0205 (0.117) | 0.0323 (0.146)
16p gain | 37 (34%) | 73 | 0.00023 (0.0361) | 0.00248 (0.0581)
20p gain | 24 (22%) | 86 | 0.0472 (0.175) | 0.04 (0.161)
1p loss | 16 (15%) | 94 | 0.0266 (0.136) | 0.0123 (0.0897)
3p loss | 36 (33%) | 74 | 0.00372 (0.0622) | 0.0299 (0.139)
3q loss | 27 (25%) | 83 | 0.00628 (0.0662) | 0.00301 (0.0581)
5q loss | 19 (17%) | 91 | 0.00163 (0.0581) | 0.00243 (0.0581)
10q loss | 28 (25%) | 82 | 0.0496 (0.175) | 0.0271 (0.136)
11p loss | 27 (25%) | 83 | 0.0102 (0.0839) | 0.011 (0.087)
16p loss | 15 (14%) | 95 | 0.00668 (0.0662) | 0.0414 (0.161)
18p loss | 40 (36%) | 70 | 0.0209 (0.117) | 0.00536 (0.0662)
18q loss | 46 (42%) | 64 | 0.0369 (0.156) | 0.012 (0.0897)
21p loss | 42 (38%) | 68 | 0.0174 (0.11) | 0.0065 (0.0662)
21q loss | 38 (35%) | 72 | 0.0201 (0.117) | 0.00306 (0.0581)
yp loss | 63 (57%) | 47 | 0.00668 (0.0662) | 0.00219 (0.0581)
yq loss | 64 (58%) | 46 | 0.0497 (0.175) | 0.00393 (0.0622)
10q gain | 7 (6%) | 103 | 0.355 (0.564) | 0.0408 (0.161)
12p gain | 23 (21%) | 87 | 0.0398 (0.161) | 0.113 (0.27)
16q gain | 28 (25%) | 82 | 0.026 (0.136) | 0.0909 (0.24)
18p gain | 8 (7%) | 102 | 0.0169 (0.11) | 0.0765 (0.229)
18q gain | 7 (6%) | 103 | 0.0433 (0.164) | 0.226 (0.413)
21q gain | 16 (15%) | 94 | 0.396 (0.593) | 0.0495 (0.175)
xp gain | 46 (42%) | 64 | 0.0365 (0.156) | 0.884 (0.933)
12p loss | 24 (22%) | 86 | 0.0948 (0.244) | 0.00201 (0.0581)
12q loss | 23 (21%) | 87 | 0.109 (0.27) | 0.00172 (0.0581)
15q loss | 52 (47%) | 58 | 0.086 (0.234) | 0.00975 (0.0839)
22p loss | 47 (43%) | 63 | 0.00553 (0.0662) | 0.521 (0.704)
22q loss | 49 (45%) | 61 | 0.00697 (0.0662) | 0.627 (0.759)
1q gain | 66 (60%) | 44 | 0.299 (0.502) | 0.455 (0.654)
3p gain | 10 (9%) | 100 | 0.765 (0.855) | 0.839 (0.901)
3q gain | 18 (16%) | 92 | 0.607 (0.744) | 0.487 (0.67)
4p gain | 8 (7%) | 102 | 1 (1.00) | 0.808 (0.884)
4q gain | 7 (6%) | 103 | 0.416 (0.608) | 0.13 (0.291)
5p gain | 57 (52%) | 53 | 0.409 (0.602) | 0.21 (0.398)
6p gain | 20 (18%) | 90 | 0.777 (0.863) | 0.326 (0.534)
6q gain | 10 (9%) | 100 | 1 (1.00) | 0.644 (0.774)
8p gain | 20 (18%) | 90 | 0.201 (0.389) | 0.861 (0.919)
8q gain | 34 (31%) | 76 | 0.604 (0.744) | 0.965 (0.996)
9p gain | 7 (6%) | 103 | 0.534 (0.704) | 0.289 (0.494)
9q gain | 5 (5%) | 105 | 1 (1.00) | 0.73 (0.834)
10p gain | 15 (14%) | 95 | 0.086 (0.234) | 0.276 (0.485)
11p gain | 21 (19%) | 89 | 0.283 (0.492) | 0.16 (0.337)
11q gain | 24 (22%) | 86 | 0.837 (0.901) | 0.561 (0.725)
12q gain | 22 (20%) | 88 | 0.0873 (0.234) | 0.232 (0.42)
13p gain | 7 (6%) | 103 | 0.537 (0.704) | 0.477 (0.661)
13q gain | 4 (4%) | 106 | 0.687 (0.796) | 0.469 (0.659)
14p gain | 26 (24%) | 84 | 0.805 (0.884) | 0.717 (0.825)
14q gain | 27 (25%) | 83 | 0.96 (0.996) | 0.142 (0.311)
15p gain | 9 (8%) | 101 | 0.109 (0.27) | 0.189 (0.382)
17p gain | 22 (20%) | 88 | 0.593 (0.744) | 0.684 (0.796)
17q gain | 30 (27%) | 80 | 0.891 (0.935) | 0.156 (0.334)
19p gain | 14 (13%) | 96 | 0.196 (0.384) | 0.314 (0.524)
19q gain | 15 (14%) | 95 | 0.266 (0.473) | 0.384 (0.579)
20q gain | 29 (26%) | 81 | 0.0546 (0.189) | 0.17 (0.35)
21p gain | 4 (4%) | 106 | 0.363 (0.564) | 0.377 (0.574)
22p gain | 4 (4%) | 106 | 0.687 (0.796) | 0.472 (0.659)
22q gain | 3 (3%) | 107 | 0.333 (0.54) | 0.259 (0.465)
xq gain | 49 (45%) | 61 | 0.103 (0.262) | 0.97 (0.996)
yp gain | 24 (22%) | 86 | 0.0657 (0.208) | 0.22 (0.406)
yq gain | 17 (15%) | 93 | 0.365 (0.564) | 0.75 (0.843)
1q loss | 6 (5%) | 104 | 0.559 (0.725) | 0.653 (0.775)
2p loss | 8 (7%) | 102 | 0.574 (0.733) | 0.472 (0.659)
2q loss | 10 (9%) | 100 | 0.362 (0.564) | 0.369 (0.565)
4p loss | 19 (17%) | 91 | 0.064 (0.207) | 0.191 (0.382)
4q loss | 19 (17%) | 91 | 0.0643 (0.207) | 0.0692 (0.216)
5p loss | 7 (6%) | 103 | 0.215 (0.401) | 0.15 (0.325)
6p loss | 19 (17%) | 91 | 0.113 (0.27) | 0.123 (0.281)
6q loss | 31 (28%) | 79 | 0.136 (0.301) | 0.119 (0.279)
7p loss | 8 (7%) | 102 | 0.46 (0.657) | 0.167 (0.348)
7q loss | 9 (8%) | 101 | 0.675 (0.796) | 0.127 (0.287)
8p loss | 33 (30%) | 77 | 0.196 (0.384) | 0.215 (0.401)
8q loss | 15 (14%) | 95 | 0.285 (0.492) | 0.295 (0.5)
9p loss | 53 (48%) | 57 | 0.538 (0.704) | 0.365 (0.564)
9q loss | 54 (49%) | 56 | 0.535 (0.704) | 0.527 (0.704)
10p loss | 26 (24%) | 84 | 0.0815 (0.231) | 0.114 (0.27)
11q loss | 22 (20%) | 88 | 0.121 (0.281) | 0.175 (0.358)
13p loss | 50 (45%) | 60 | 0.354 (0.564) | 0.832 (0.901)
13q loss | 48 (44%) | 62 | 0.586 (0.743) | 0.0726 (0.222)
14p loss | 34 (31%) | 76 | 0.931 (0.972) | 0.32 (0.529)
14q loss | 10 (9%) | 100 | 0.0772 (0.229) | 0.407 (0.602)
15p loss | 58 (53%) | 52 | 0.0942 (0.244) | 0.0558 (0.189)
16q loss | 24 (22%) | 86 | 0.0786 (0.229) | 0.084 (0.234)
17p loss | 24 (22%) | 86 | 0.511 (0.698) | 1 (1.00)
17q loss | 18 (16%) | 92 | 1 (1.00) | 0.575 (0.733)
19p loss | 45 (41%) | 65 | 0.0638 (0.207) | 0.0794 (0.229)
19q loss | 35 (32%) | 75 | 0.81 (0.884) | 0.733 (0.834)
20p loss | 26 (24%) | 84 | 0.597 (0.744) | 0.206 (0.396)
20q loss | 21 (19%) | 89 | 0.744 (0.842) | 0.648 (0.774)
xp loss | 13 (12%) | 97 | 0.867 (0.92) | 0.612 (0.745)
xq loss | 11 (10%) | 99 | 0.602 (0.744) | 0.435 (0.631)

'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.12

Table S1. Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
1P GAIN MUTATED | 5 | 6 | 21
1P GAIN WILD-TYPE | 28 | 21 | 29

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'1p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.14

Table S2. Gene #1: '1p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
1P GAIN MUTATED | 7 | 5 | 20
1P GAIN WILD-TYPE | 26 | 25 | 27

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00555 (Fisher's exact test), Q value = 0.066

Table S3. Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
2P GAIN MUTATED | 12 | 7 | 4
2P GAIN WILD-TYPE | 21 | 20 | 46

Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.11

Table S4. Gene #3: '2p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
2P GAIN MUTATED | 10 | 9 | 4
2P GAIN WILD-TYPE | 23 | 21 | 43

Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.11

Table S5. Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
2Q GAIN MUTATED | 10 | 7 | 4
2Q GAIN WILD-TYPE | 23 | 20 | 46

Figure S5. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.16

Table S6. Gene #4: '2q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
2Q GAIN MUTATED | 8 | 9 | 4
2Q GAIN WILD-TYPE | 25 | 21 | 43

Figure S6. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'5q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.11

Table S7. Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
5Q GAIN MUTATED | 3 | 5 | 18
5Q GAIN WILD-TYPE | 30 | 22 | 32

Figure S7. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'5q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.036

Table S8. Gene #10: '5q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
5Q GAIN MUTATED | 3 | 3 | 20
5Q GAIN WILD-TYPE | 30 | 27 | 27

Figure S8. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.14

Table S9. Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
7P GAIN MUTATED | 11 | 17 | 30
7P GAIN WILD-TYPE | 22 | 10 | 20

Figure S9. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00974 (Fisher's exact test), Q value = 0.084

Table S10. Gene #13: '7p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
7P GAIN MUTATED | 10 | 19 | 29
7P GAIN WILD-TYPE | 23 | 11 | 18

Figure S10. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.12

Table S11. Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
7Q GAIN MUTATED | 9 | 17 | 22
7Q GAIN WILD-TYPE | 24 | 10 | 28

Figure S11. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.15

Table S12. Gene #14: '7q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
7Q GAIN MUTATED | 9 | 18 | 21
7Q GAIN WILD-TYPE | 24 | 12 | 26

Figure S12. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'10q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.16

Table S13. Gene #20: '10q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
10Q GAIN MUTATED | 5 | 0 | 2
10Q GAIN WILD-TYPE | 28 | 30 | 45

Figure S13. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 0.16

Table S14. Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
12P GAIN MUTATED | 12 | 3 | 8
12P GAIN WILD-TYPE | 21 | 24 | 42

Figure S14. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.036

Table S15. Gene #30: '16p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
16P GAIN MUTATED | 5 | 5 | 27
16P GAIN WILD-TYPE | 28 | 22 | 23

Figure S15. Get High-res Image Gene #30: '16p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.058

Table S16. Gene #30: '16p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
16P GAIN MUTATED | 5 | 8 | 24
16P GAIN WILD-TYPE | 28 | 22 | 23

Figure S16. Get High-res Image Gene #30: '16p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.14

Table S17. Gene #31: '16q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
16Q GAIN MUTATED | 5 | 4 | 19
16Q GAIN WILD-TYPE | 28 | 23 | 31

Figure S17. Get High-res Image Gene #31: '16q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.11

Table S18. Gene #34: '18p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
18P GAIN MUTATED | 6 | 1 | 1
18P GAIN WILD-TYPE | 27 | 26 | 49

Figure S18. Get High-res Image Gene #34: '18p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.16

Table S19. Gene #35: '18q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
18Q GAIN MUTATED | 5 | 1 | 1
18Q GAIN WILD-TYPE | 28 | 26 | 49

Figure S19. Get High-res Image Gene #35: '18q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.17

Table S20. Gene #38: '20p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
20P GAIN MUTATED | 11 | 7 | 6
20P GAIN WILD-TYPE | 22 | 20 | 44

Figure S20. Get High-res Image Gene #38: '20p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.16

Table S21. Gene #38: '20p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
20P GAIN MUTATED | 10 | 9 | 5
20P GAIN WILD-TYPE | 23 | 21 | 42

Figure S21. Get High-res Image Gene #38: '20p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'21q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.17

Table S22. Gene #41: '21q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
21Q GAIN MUTATED | 1 | 5 | 10
21Q GAIN WILD-TYPE | 32 | 25 | 37

Figure S22. Get High-res Image Gene #41: '21q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'xp gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.16

Table S23. Gene #44: 'xp gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
XP GAIN MUTATED | 18 | 6 | 22
XP GAIN WILD-TYPE | 15 | 21 | 28

Figure S23. Get High-res Image Gene #44: 'xp gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.14

Table S24. Gene #48: '1p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
1P LOSS MUTATED | 9 | 4 | 3
1P LOSS WILD-TYPE | 24 | 23 | 47

Figure S24. Get High-res Image Gene #48: '1p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.09

Table S25. Gene #48: '1p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
1P LOSS MUTATED | 9 | 5 | 2
1P LOSS WILD-TYPE | 24 | 25 | 45

Figure S25. Get High-res Image Gene #48: '1p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00372 (Fisher's exact test), Q value = 0.062

Table S26. Gene #52: '3p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
3P LOSS MUTATED | 17 | 3 | 16
3P LOSS WILD-TYPE | 16 | 24 | 34

Figure S26. Get High-res Image Gene #52: '3p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.14

Table S27. Gene #52: '3p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
3P LOSS MUTATED | 16 | 5 | 15
3P LOSS WILD-TYPE | 17 | 25 | 32

Figure S27. Get High-res Image Gene #52: '3p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00628 (Fisher's exact test), Q value = 0.066

Table S28. Gene #53: '3q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
3Q LOSS MUTATED | 14 | 2 | 11
3Q LOSS WILD-TYPE | 19 | 25 | 39

Figure S28. Get High-res Image Gene #53: '3q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00301 (Fisher's exact test), Q value = 0.058

Table S29. Gene #53: '3q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
3Q LOSS MUTATED | 15 | 3 | 9
3Q LOSS WILD-TYPE | 18 | 27 | 38

Figure S29. Get High-res Image Gene #53: '3q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.058

Table S30. Gene #57: '5q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
5Q LOSS MUTATED | 9 | 8 | 2
5Q LOSS WILD-TYPE | 24 | 19 | 48

Figure S30. Get High-res Image Gene #57: '5q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.058

Table S31. Gene #57: '5q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
5Q LOSS MUTATED | 7 | 10 | 2
5Q LOSS WILD-TYPE | 26 | 20 | 45

Figure S31. Get High-res Image Gene #57: '5q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.17

Table S32. Gene #67: '10q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
10Q LOSS MUTATED | 4 | 6 | 18
10Q LOSS WILD-TYPE | 29 | 21 | 32

Figure S32. Get High-res Image Gene #67: '10q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.14

Table S33. Gene #67: '10q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
10Q LOSS MUTATED | 3 | 9 | 16
10Q LOSS WILD-TYPE | 30 | 21 | 31

Figure S33. Get High-res Image Gene #67: '10q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.084

Table S34. Gene #68: '11p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
11P LOSS MUTATED | 10 | 11 | 6
11P LOSS WILD-TYPE | 23 | 16 | 44

Figure S34. Get High-res Image Gene #68: '11p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.087

Table S35. Gene #68: '11p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
11P LOSS MUTATED | 8 | 13 | 6
11P LOSS WILD-TYPE | 25 | 17 | 41

Figure S35. Get High-res Image Gene #68: '11p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'12p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.058

Table S36. Gene #70: '12p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
12P LOSS MUTATED | 1 | 7 | 16
12P LOSS WILD-TYPE | 32 | 23 | 31

Figure S36. Get High-res Image Gene #70: '12p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'12q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.058

Table S37. Gene #71: '12q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
12Q LOSS MUTATED | 1 | 6 | 16
12Q LOSS WILD-TYPE | 32 | 24 | 31

Figure S37. Get High-res Image Gene #71: '12q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'15q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00975 (Fisher's exact test), Q value = 0.084

Table S38. Gene #77: '15q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
15Q LOSS MUTATED | 9 | 14 | 29
15Q LOSS WILD-TYPE | 24 | 16 | 18

Figure S38. Get High-res Image Gene #77: '15q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'16p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00668 (Fisher's exact test), Q value = 0.066

Table S39. Gene #78: '16p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
16P LOSS MUTATED | 5 | 8 | 2
16P LOSS WILD-TYPE | 28 | 19 | 48

Figure S39. Get High-res Image Gene #78: '16p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'16p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.16

Table S40. Gene #78: '16p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
16P LOSS MUTATED | 4 | 8 | 3
16P LOSS WILD-TYPE | 29 | 22 | 44

Figure S40. Get High-res Image Gene #78: '16p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.12

Table S41. Gene #82: '18p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
18P LOSS MUTATED | 6 | 10 | 24
18P LOSS WILD-TYPE | 27 | 17 | 26

Figure S41. Get High-res Image Gene #82: '18p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00536 (Fisher's exact test), Q value = 0.066

Table S42. Gene #82: '18p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
18P LOSS MUTATED | 5 | 12 | 23
18P LOSS WILD-TYPE | 28 | 18 | 24

Figure S42. Get High-res Image Gene #82: '18p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.16

Table S43. Gene #83: '18q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
18Q LOSS MUTATED | 8 | 12 | 26
18Q LOSS WILD-TYPE | 25 | 15 | 24

Figure S43. Get High-res Image Gene #83: '18q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.09

Table S44. Gene #83: '18q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
18Q LOSS MUTATED | 7 | 14 | 25
18Q LOSS WILD-TYPE | 26 | 16 | 22

Figure S44. Get High-res Image Gene #83: '18q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'21p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.11

Table S45. Gene #88: '21p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
21P LOSS MUTATED | 19 | 10 | 13
21P LOSS WILD-TYPE | 14 | 17 | 37

Figure S45. Get High-res Image Gene #88: '21p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'21p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0065 (Fisher's exact test), Q value = 0.066

Table S46. Gene #88: '21p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
21P LOSS MUTATED | 17 | 15 | 10
21P LOSS WILD-TYPE | 16 | 15 | 37

Figure S46. Get High-res Image Gene #88: '21p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.12

Table S47. Gene #89: '21q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
21Q LOSS MUTATED | 17 | 10 | 11
21Q LOSS WILD-TYPE | 16 | 17 | 39

Figure S47. Get High-res Image Gene #89: '21q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.058

Table S48. Gene #89: '21q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
21Q LOSS MUTATED | 16 | 14 | 8
21Q LOSS WILD-TYPE | 17 | 16 | 39

Figure S48. Get High-res Image Gene #89: '21q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'22p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00553 (Fisher's exact test), Q value = 0.066

Table S49. Gene #90: '22p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
22P LOSS MUTATED | 21 | 12 | 14
22P LOSS WILD-TYPE | 12 | 15 | 36

Figure S49. Get High-res Image Gene #90: '22p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00697 (Fisher's exact test), Q value = 0.066

Table S50. Gene #91: '22q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
22Q LOSS MUTATED | 22 | 11 | 16
22Q LOSS WILD-TYPE | 11 | 16 | 34

Figure S50. Get High-res Image Gene #91: '22q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'yp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00668 (Fisher's exact test), Q value = 0.066

Table S51. Gene #94: 'yp loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
YP LOSS MUTATED | 25 | 17 | 21
YP LOSS WILD-TYPE | 8 | 10 | 29

Figure S51. Get High-res Image Gene #94: 'yp loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'yp loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.058

Table S52. Gene #94: 'yp loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
YP LOSS MUTATED | 25 | 20 | 18
YP LOSS WILD-TYPE | 8 | 10 | 29

Figure S52. Get High-res Image Gene #94: 'yp loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'yq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0497 (Fisher's exact test), Q value = 0.17

Table S53. Gene #95: 'yq loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
YQ LOSS MUTATED | 24 | 17 | 23
YQ LOSS WILD-TYPE | 9 | 10 | 27

Figure S53. Get High-res Image Gene #95: 'yq loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'yq loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00393 (Fisher's exact test), Q value = 0.062

Table S54. Gene #95: 'yq loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
YQ LOSS MUTATED | 25 | 20 | 19
YQ LOSS WILD-TYPE | 8 | 10 | 28

Figure S54. Get High-res Image Gene #95: 'yq loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

Methods & Data
Input

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

- Processed Copy number data file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/038fcf2f-32c7-437e-beb7-ded16a017a25/correlate_genomic_events_all/d2cdaeae-8d2e-46f5-b7bd-6cd908ffe652/call-preprocess_genomic_event/transformed.cor.cli.txt

- Molecular subtypes file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/69dd18b3-97fe-4143-b0f4-32e5d55e929d/aggregate_clusters_workflow/d44c315a-761b-4b72-be1f-cb969be36102/call-aggregate_clusters/CPTAC3-LUAD-TP.transposedmergedcluster.txt

- Number of patients = 110

- Number of significantly arm-level cnvs = 95

- Number of molecular subtypes = 2

- Exclude genes that fewer than K tumors have mutations, 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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