Correlation between copy number variation genes (focal events) and molecular subtypes
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)
Made with Nozzle