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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