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

Summary

Testing the association between copy number variation 51 focal events and 2 molecular subtypes across 110 patients, 31 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_1p34.2 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- amp_4q12 cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- amp_5q35.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- amp_7p11.2 cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- amp_13q31.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- amp_17q23.1 cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- amp_20p11.21 cnv correlated to 'MRNA_CHIERARCHICAL'.

- amp_xp22.33 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- del_3p24.1 cnv correlated to 'MRNA_CHIERARCHICAL'.

- del_4q35.2 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- del_5q15 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- del_6q16.3 cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- del_10q25.1 cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- del_12p13.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- del_13q11 cnv correlated to 'LINCRNA_CHIERARCHICAL'.

- del_18q21.31 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- del_19q13.33 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- del_21p11.2 cnv correlated to 'MRNA_CHIERARCHICAL'.

- del_21q11.2 cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- del_xq28 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 51 focal 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, 31 significant findings detected.

|  | Clinical Features | MRNA CHIERARCHICAL | LINCRNA CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test
amp 1p34 2 | 26 (24%) | 84 | 0.0228 (0.0971) | 0.00713 (0.0589)
amp 5q35 1 | 35 (32%) | 75 | 0.00347 (0.0354) | 0.0001 (0.0102)
amp 13q31 1 | 30 (27%) | 80 | 0.00292 (0.0331) | 0.00887 (0.0589)
amp xp22 33 | 46 (42%) | 64 | 0.0179 (0.0842) | 0.00881 (0.0589)
del 4q35 2 | 37 (34%) | 73 | 0.0114 (0.0614) | 0.0108 (0.0614)
del 5q15 | 43 (39%) | 67 | 0.0342 (0.129) | 0.00191 (0.0278)
del 12p13 1 | 44 (40%) | 66 | 0.0283 (0.111) | 0.00085 (0.0173)
del 18q21 31 | 61 (55%) | 49 | 0.0283 (0.111) | 0.00166 (0.0278)
del 19q13 33 | 43 (39%) | 67 | 0.00949 (0.0589) | 0.0354 (0.129)
del 21q11 2 | 25 (23%) | 85 | 0.00901 (0.0589) | 0.00083 (0.0173)
del xq28 | 24 (22%) | 86 | 0.00053 (0.0173) | 0.00981 (0.0589)
amp 4q12 | 20 (18%) | 90 | 0.234 (0.451) | 0.0396 (0.135)
amp 7p11 2 | 63 (57%) | 47 | 0.133 (0.332) | 0.00063 (0.0173)
amp 17q23 1 | 54 (49%) | 56 | 0.252 (0.46) | 0.00517 (0.0479)
amp 20p11 21 | 27 (25%) | 83 | 0.0199 (0.0885) | 0.0654 (0.19)
del 3p24 1 | 53 (48%) | 57 | 0.0155 (0.0789) | 0.673 (0.789)
del 6q16 3 | 58 (53%) | 52 | 0.456 (0.628) | 0.0477 (0.157)
del 10q25 1 | 39 (35%) | 71 | 0.103 (0.263) | 0.00219 (0.0279)
del 13q11 | 64 (58%) | 46 | 0.345 (0.542) | 0.0385 (0.135)
del 21p11 2 | 66 (60%) | 44 | 0.0182 (0.0842) | 0.0564 (0.174)
amp 1q21 2 | 89 (81%) | 21 | 0.744 (0.842) | 0.822 (0.892)
amp 5p15 33 | 76 (69%) | 34 | 0.224 (0.444) | 0.207 (0.422)
amp 6p21 1 | 44 (40%) | 66 | 0.617 (0.74) | 0.401 (0.583)
amp 6q27 | 41 (37%) | 69 | 0.848 (0.904) | 0.3 (0.502)
amp 8q13 1 | 47 (43%) | 63 | 0.881 (0.909) | 0.61 (0.74)
amp 8q24 21 | 65 (59%) | 45 | 0.176 (0.383) | 0.085 (0.228)
amp 8q24 3 | 69 (63%) | 41 | 0.611 (0.74) | 0.262 (0.46)
amp 11q13 3 | 46 (42%) | 64 | 0.531 (0.695) | 0.756 (0.842)
amp 12p13 33 | 54 (49%) | 56 | 0.167 (0.369) | 0.809 (0.888)
amp 12p11 21 | 37 (34%) | 73 | 0.553 (0.705) | 0.759 (0.842)
amp 12q15 | 33 (30%) | 77 | 0.293 (0.502) | 0.163 (0.369)
amp 14q13 3 | 62 (56%) | 48 | 0.663 (0.787) | 0.226 (0.444)
amp 14q32 33 | 46 (42%) | 64 | 0.577 (0.727) | 0.687 (0.796)
amp 19q12 | 33 (30%) | 77 | 0.331 (0.536) | 0.299 (0.502)
amp 20q13 2 | 51 (46%) | 59 | 0.97 (0.979) | 0.857 (0.904)
amp 20q13 33 | 51 (46%) | 59 | 0.399 (0.583) | 1 (1.00)
amp 21p12 | 24 (22%) | 86 | 0.253 (0.46) | 0.0686 (0.19)
amp xq27 3 | 60 (55%) | 50 | 0.429 (0.599) | 0.735 (0.842)
amp yq11 223 | 25 (23%) | 85 | 0.586 (0.729) | 0.261 (0.46)
del 1p13 3 | 38 (35%) | 72 | 0.522 (0.695) | 0.155 (0.359)
del 6p11 2 | 12 (11%) | 98 | 0.859 (0.904) | 0.927 (0.946)
del 8p23 1 | 58 (53%) | 52 | 0.417 (0.591) | 0.203 (0.422)
del 9p23 | 63 (57%) | 47 | 0.529 (0.695) | 0.461 (0.628)
del 9p21 3 | 67 (61%) | 43 | 0.553 (0.705) | 0.359 (0.555)
del 15q13 1 | 64 (58%) | 46 | 0.882 (0.909) | 0.391 (0.583)
del 16q24 3 | 42 (38%) | 68 | 0.185 (0.393) | 0.139 (0.338)
del 17p13 1 | 75 (68%) | 35 | 0.0627 (0.188) | 0.0531 (0.169)
del 22p11 2 | 44 (40%) | 66 | 0.152 (0.359) | 0.0691 (0.19)
del 22q13 32 | 55 (50%) | 55 | 0.345 (0.542) | 0.379 (0.577)
del xp22 33 | 23 (21%) | 87 | 0.406 (0.583) | 0.331 (0.536)
del yq11 223 | 69 (63%) | 41 | 0.244 (0.46) | 0.095 (0.249)

'amp_1p34.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.097

Table S1. Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
AMP PEAK 1(1P34.2) MUTATED | 5 | 3 | 18
AMP PEAK 1(1P34.2) WILD-TYPE | 28 | 24 | 32

Figure S1. Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'amp_1p34.2' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00713 (Fisher's exact test), Q value = 0.059

Table S2. Gene #1: 'amp_1p34.2' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
AMP PEAK 1(1P34.2) MUTATED | 5 | 3 | 18
AMP PEAK 1(1P34.2) WILD-TYPE | 28 | 27 | 29

Figure S2. Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'amp_4q12' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.13

Table S3. Gene #3: 'amp_4q12' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
AMP PEAK 3(4Q12) MUTATED | 2 | 9 | 9
AMP PEAK 3(4Q12) WILD-TYPE | 31 | 21 | 38

Figure S3. Get High-res Image Gene #3: 'amp_4q12' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'amp_5q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00347 (Fisher's exact test), Q value = 0.035

Table S4. Gene #5: 'amp_5q35.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
AMP PEAK 5(5Q35.1) MUTATED | 5 | 6 | 24
AMP PEAK 5(5Q35.1) WILD-TYPE | 28 | 21 | 26

Figure S4. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'amp_5q35.1' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.01

Table S5. Gene #5: 'amp_5q35.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
AMP PEAK 5(5Q35.1) MUTATED | 3 | 7 | 25
AMP PEAK 5(5Q35.1) WILD-TYPE | 30 | 23 | 22

Figure S5. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'amp_7p11.2' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.017

Table S6. Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
AMP PEAK 8(7P11.2) MUTATED | 10 | 23 | 30
AMP PEAK 8(7P11.2) WILD-TYPE | 23 | 7 | 17

Figure S6. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'amp_13q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00292 (Fisher's exact test), Q value = 0.033

Table S7. Gene #16: 'amp_13q31.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
AMP PEAK 16(13Q31.1) MUTATED | 7 | 2 | 21
AMP PEAK 16(13Q31.1) WILD-TYPE | 26 | 25 | 29

Figure S7. Get High-res Image Gene #16: 'amp_13q31.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'amp_13q31.1' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00887 (Fisher's exact test), Q value = 0.059

Table S8. Gene #16: 'amp_13q31.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
AMP PEAK 16(13Q31.1) MUTATED | 6 | 4 | 20
AMP PEAK 16(13Q31.1) WILD-TYPE | 27 | 26 | 27

Figure S8. Get High-res Image Gene #16: 'amp_13q31.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'amp_17q23.1' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00517 (Fisher's exact test), Q value = 0.048

Table S9. Gene #19: 'amp_17q23.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
AMP PEAK 19(17Q23.1) MUTATED | 9 | 20 | 25
AMP PEAK 19(17Q23.1) WILD-TYPE | 24 | 10 | 22

Figure S9. Get High-res Image Gene #19: 'amp_17q23.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.088

Table S10. Gene #21: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
AMP PEAK 21(20P11.21) MUTATED | 14 | 5 | 8
AMP PEAK 21(20P11.21) WILD-TYPE | 19 | 22 | 42

Figure S10. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'amp_xp22.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.084

Table S11. Gene #25: 'amp_xp22.33' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
AMP PEAK 25(XP22.33) MUTATED | 11 | 7 | 28
AMP PEAK 25(XP22.33) WILD-TYPE | 22 | 20 | 22

Figure S11. Get High-res Image Gene #25: 'amp_xp22.33' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'amp_xp22.33' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00881 (Fisher's exact test), Q value = 0.059

Table S12. Gene #25: 'amp_xp22.33' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
AMP PEAK 25(XP22.33) MUTATED | 12 | 7 | 27
AMP PEAK 25(XP22.33) WILD-TYPE | 21 | 23 | 20

Figure S12. Get High-res Image Gene #25: 'amp_xp22.33' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_3p24.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.079

Table S13. Gene #29: 'del_3p24.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
DEL PEAK 2(3P24.1) MUTATED | 22 | 8 | 23
DEL PEAK 2(3P24.1) WILD-TYPE | 11 | 19 | 27

Figure S13. Get High-res Image Gene #29: 'del_3p24.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_4q35.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.061

Table S14. Gene #30: 'del_4q35.2' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
DEL PEAK 3(4Q35.2) MUTATED | 18 | 6 | 13
DEL PEAK 3(4Q35.2) WILD-TYPE | 15 | 21 | 37

Figure S14. Get High-res Image Gene #30: 'del_4q35.2' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_4q35.2' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.061

Table S15. Gene #30: 'del_4q35.2' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 3(4Q35.2) MUTATED | 18 | 8 | 11
DEL PEAK 3(4Q35.2) WILD-TYPE | 15 | 22 | 36

Figure S15. Get High-res Image Gene #30: 'del_4q35.2' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_5q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.13

Table S16. Gene #31: 'del_5q15' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
DEL PEAK 4(5Q15) MUTATED | 16 | 14 | 13
DEL PEAK 4(5Q15) WILD-TYPE | 17 | 13 | 37

Figure S16. Get High-res Image Gene #31: 'del_5q15' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_5q15' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00191 (Fisher's exact test), Q value = 0.028

Table S17. Gene #31: 'del_5q15' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 4(5Q15) MUTATED | 15 | 18 | 10
DEL PEAK 4(5Q15) WILD-TYPE | 18 | 12 | 37

Figure S17. Get High-res Image Gene #31: 'del_5q15' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_6q16.3' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.16

Table S18. Gene #33: 'del_6q16.3' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 6(6Q16.3) MUTATED | 13 | 21 | 24
DEL PEAK 6(6Q16.3) WILD-TYPE | 20 | 9 | 23

Figure S18. Get High-res Image Gene #33: 'del_6q16.3' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_10q25.1' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.028

Table S19. Gene #37: 'del_10q25.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 10(10Q25.1) MUTATED | 4 | 13 | 22
DEL PEAK 10(10Q25.1) WILD-TYPE | 29 | 17 | 25

Figure S19. Get High-res Image Gene #37: 'del_10q25.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_12p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.11

Table S20. Gene #38: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
DEL PEAK 11(12P13.1) MUTATED | 7 | 12 | 25
DEL PEAK 11(12P13.1) WILD-TYPE | 26 | 15 | 25

Figure S20. Get High-res Image Gene #38: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_12p13.1' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.017

Table S21. Gene #38: 'del_12p13.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 11(12P13.1) MUTATED | 5 | 13 | 26
DEL PEAK 11(12P13.1) WILD-TYPE | 28 | 17 | 21

Figure S21. Get High-res Image Gene #38: 'del_12p13.1' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_13q11' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.13

Table S22. Gene #39: 'del_13q11' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 12(13Q11) MUTATED | 15 | 23 | 26
DEL PEAK 12(13Q11) WILD-TYPE | 18 | 7 | 21

Figure S22. Get High-res Image Gene #39: 'del_13q11' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_18q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.11

Table S23. Gene #43: 'del_18q21.31' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
DEL PEAK 16(18Q21.31) MUTATED | 12 | 16 | 33
DEL PEAK 16(18Q21.31) WILD-TYPE | 21 | 11 | 17

Figure S23. Get High-res Image Gene #43: 'del_18q21.31' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_18q21.31' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.028

Table S24. Gene #43: 'del_18q21.31' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 16(18Q21.31) MUTATED | 10 | 18 | 33
DEL PEAK 16(18Q21.31) WILD-TYPE | 23 | 12 | 14

Figure S24. Get High-res Image Gene #43: 'del_18q21.31' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_19q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00949 (Fisher's exact test), Q value = 0.059

Table S25. Gene #44: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
DEL PEAK 17(19Q13.33) MUTATED | 6 | 14 | 23
DEL PEAK 17(19Q13.33) WILD-TYPE | 27 | 13 | 27

Figure S25. Get High-res Image Gene #44: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_19q13.33' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.13

Table S26. Gene #44: 'del_19q13.33' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 17(19Q13.33) MUTATED | 7 | 13 | 23
DEL PEAK 17(19Q13.33) WILD-TYPE | 26 | 17 | 24

Figure S26. Get High-res Image Gene #44: 'del_19q13.33' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_21p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.084

Table S27. Gene #45: 'del_21p11.2' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
DEL PEAK 18(21P11.2) MUTATED | 26 | 16 | 24
DEL PEAK 18(21P11.2) WILD-TYPE | 7 | 11 | 26

Figure S27. Get High-res Image Gene #45: 'del_21p11.2' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00901 (Fisher's exact test), Q value = 0.059

Table S28. Gene #46: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
DEL PEAK 19(21Q11.2) MUTATED | 12 | 8 | 5
DEL PEAK 19(21Q11.2) WILD-TYPE | 21 | 19 | 45

Figure S28. Get High-res Image Gene #46: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_21q11.2' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.017

Table S29. Gene #46: 'del_21q11.2' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 19(21Q11.2) MUTATED | 11 | 11 | 3
DEL PEAK 19(21Q11.2) WILD-TYPE | 22 | 19 | 44

Figure S29. Get High-res Image Gene #46: 'del_21q11.2' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'del_xq28' versus 'MRNA_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.017

Table S30. Gene #50: 'del_xq28' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 27 | 50
DEL PEAK 23(XQ28) MUTATED | 12 | 9 | 3
DEL PEAK 23(XQ28) WILD-TYPE | 21 | 18 | 47

Figure S30. Get High-res Image Gene #50: 'del_xq28' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_xq28' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00981 (Fisher's exact test), Q value = 0.059

Table S31. Gene #50: 'del_xq28' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 30 | 47
DEL PEAK 23(XQ28) MUTATED | 11 | 9 | 4
DEL PEAK 23(XQ28) WILD-TYPE | 22 | 21 | 43

Figure S31. Get High-res Image Gene #50: 'del_xq28' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

Methods & Data
Input

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

- Processed Copy number data file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/601c74c2-1f3b-4ccc-a955-3c502815f156/correlate_genomic_events_all/3ed33866-fb34-41f2-a6ce-5a5fef54acd2/call-preprocess_genomic_event/transformed.cor.cli.txt

- Molecular subtype 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 focal cnvs = 51

- Number of molecular subtypes = 2

- 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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