Correlation between copy number variation genes and molecular subtypes

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 48 peak regions and 8 molecular subtypes across 83 patients, 34 significant findings detected with Q value < 0.25.

Amp Peak 1(1p32.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(6p21.1) cnvs correlated to 'METHLYATION_CNMF'.
Amp Peak 5(6q24.3) cnvs correlated to 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 9(12q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 1(1p36.32) cnvs correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 2(1p32.3) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q37.3) cnvs correlated to 'CN_CNMF'.
Del Peak 13(9p24.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 14(9p21.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 17(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 22(13q14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 30(19q13.33) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 32(22q13.32) cnvs correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 48 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 34 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 9(12q15)	0 (0%)	43	3.02e-10 (1.16e-07)	5.12e-10 (1.95e-07)	1.58e-08 (5.96e-06)	3.89e-10 (1.49e-07)	8.35e-09 (3.16e-06)	3.35e-08 (1.26e-05)	6.66e-12 (2.56e-09)	2.32e-09 (8.81e-07)
Del Peak 1(1p36 32)	0 (0%)	56	0.146 (1.00)	0.00102 (0.358)	0.00138 (0.475)	0.000532 (0.19)	0.000306 (0.11)	0.000215 (0.0777)	0.000668 (0.235)	7.27e-05 (0.027)
Del Peak 14(9p21 3)	0 (0%)	46	1.33e-07 (5e-05)	0.0121 (1.00)	0.000693 (0.243)	8.77e-05 (0.0324)	0.0185 (1.00)	0.212 (1.00)	8.97e-05 (0.0331)	0.22 (1.00)
Del Peak 17(10q23 31)	0 (0%)	42	0.000107 (0.0391)	0.000219 (0.0792)	0.0039 (1.00)	0.000587 (0.207)	0.00433 (1.00)	0.00293 (0.971)	0.00133 (0.459)	0.000573 (0.204)
Amp Peak 5(6q24 3)	0 (0%)	56	0.00264 (0.879)	0.000521 (0.186)	0.00162 (0.552)	0.00222 (0.748)	0.00789 (1.00)	0.00047 (0.169)	0.000193 (0.0705)	0.00112 (0.391)
Del Peak 13(9p24 3)	0 (0%)	50	1.96e-06 (0.000735)	0.0199 (1.00)	0.011 (1.00)	0.000499 (0.179)	0.06 (1.00)	0.0514 (1.00)	0.00186 (0.63)	0.0876 (1.00)
Del Peak 22(13q14 2)	0 (0%)	24	0.000194 (0.0706)	6.44e-05 (0.0239)	0.0186 (1.00)	0.00885 (1.00)	0.00566 (1.00)	0.0194 (1.00)	0.00505 (1.00)	0.00867 (1.00)
Amp Peak 1(1p32 1)	0 (0%)	55	0.000208 (0.0754)	0.00343 (1.00)	0.506 (1.00)	0.165 (1.00)	0.0912 (1.00)	0.0136 (1.00)	0.0573 (1.00)	0.017 (1.00)
Amp Peak 4(6p21 1)	0 (0%)	62	0.0105 (1.00)	9.19e-05 (0.0338)	0.131 (1.00)	0.0101 (1.00)	0.00882 (1.00)	0.0144 (1.00)	0.00279 (0.928)	0.0114 (1.00)
Del Peak 2(1p32 3)	0 (0%)	68	1.95e-05 (0.00728)	0.938 (1.00)	0.444 (1.00)	0.805 (1.00)	0.282 (1.00)	0.366 (1.00)	0.551 (1.00)	0.821 (1.00)
Del Peak 5(2q37 3)	0 (0%)	47	0.00011 (0.0403)	0.028 (1.00)	0.0813 (1.00)	0.553 (1.00)	0.664 (1.00)	0.204 (1.00)	0.55 (1.00)	0.145 (1.00)
Del Peak 30(19q13 33)	0 (0%)	53	0.0859 (1.00)	2.41e-05 (0.00898)	0.653 (1.00)	0.132 (1.00)	0.387 (1.00)	0.621 (1.00)	0.17 (1.00)	0.289 (1.00)
Del Peak 32(22q13 32)	0 (0%)	49	0.0431 (1.00)	0.000586 (0.207)	0.0402 (1.00)	0.692 (1.00)	0.495 (1.00)	0.218 (1.00)	0.13 (1.00)	0.55 (1.00)
Amp Peak 2(1q24 3)	0 (0%)	49	0.00514 (1.00)	0.41 (1.00)	0.743 (1.00)	0.692 (1.00)	0.213 (1.00)	0.627 (1.00)	0.687 (1.00)	0.419 (1.00)
Amp Peak 3(5p15 33)	0 (0%)	51	0.00478 (1.00)	0.225 (1.00)	0.183 (1.00)	0.0425 (1.00)	0.221 (1.00)	0.324 (1.00)	0.0463 (1.00)	0.249 (1.00)
Amp Peak 6(7p21 3)	0 (0%)	55	0.162 (1.00)	0.0307 (1.00)	0.0301 (1.00)	0.0558 (1.00)	0.0314 (1.00)	0.0544 (1.00)	0.0192 (1.00)	0.0712 (1.00)
Amp Peak 7(11q22 2)	0 (0%)	67	0.585 (1.00)	0.25 (1.00)	0.398 (1.00)	0.294 (1.00)	0.245 (1.00)	0.143 (1.00)	0.0731 (1.00)	0.071 (1.00)
Amp Peak 8(12p12 1)	0 (0%)	60	0.0491 (1.00)	0.378 (1.00)	0.277 (1.00)	0.595 (1.00)	0.0182 (1.00)	0.63 (1.00)	0.0603 (1.00)	0.856 (1.00)
Amp Peak 10(17p11 2)	0 (0%)	54	0.0357 (1.00)	0.00522 (1.00)	0.864 (1.00)	0.304 (1.00)	0.0411 (1.00)	0.544 (1.00)	0.639 (1.00)	0.275 (1.00)
Amp Peak 11(19p13 2)	0 (0%)	52	0.021 (1.00)	0.633 (1.00)	0.0999 (1.00)	0.422 (1.00)	0.553 (1.00)	0.915 (1.00)	0.713 (1.00)	0.459 (1.00)
Amp Peak 12(19q12)	0 (0%)	57	0.0321 (1.00)	0.000969 (0.339)	0.7 (1.00)	0.182 (1.00)	0.194 (1.00)	0.671 (1.00)	0.196 (1.00)	0.308 (1.00)
Amp Peak 13(Xq21 1)	0 (0%)	67	0.0042 (1.00)	0.106 (1.00)	0.142 (1.00)	0.827 (1.00)	0.0617 (1.00)	1 (1.00)	0.0244 (1.00)	1 (1.00)
Del Peak 3(1q44)	0 (0%)	54	0.00189 (0.639)	0.0703 (1.00)	0.0441 (1.00)	0.0632 (1.00)	0.293 (1.00)	0.379 (1.00)	0.0629 (1.00)	0.278 (1.00)
Del Peak 4(2p25 3)	0 (0%)	57	0.0193 (1.00)	0.0312 (1.00)	0.126 (1.00)	0.0154 (1.00)	0.0143 (1.00)	0.00681 (1.00)	0.00151 (0.516)	0.00228 (0.764)
Del Peak 6(3p21 31)	0 (0%)	62	0.00124 (0.43)	0.0407 (1.00)	0.0763 (1.00)	0.0101 (1.00)	0.00488 (1.00)	0.0083 (1.00)	0.0716 (1.00)	0.0815 (1.00)
Del Peak 7(3q25 2)	0 (0%)	61	0.0153 (1.00)	0.00126 (0.434)	0.0237 (1.00)	0.0126 (1.00)	0.159 (1.00)	0.00452 (1.00)	0.0194 (1.00)	0.00672 (1.00)
Del Peak 8(4q34 3)	0 (0%)	48	0.0436 (1.00)	0.022 (1.00)	0.102 (1.00)	0.408 (1.00)	0.444 (1.00)	0.912 (1.00)	0.524 (1.00)	0.64 (1.00)
Del Peak 9(6p24 3)	0 (0%)	53	0.548 (1.00)	0.0308 (1.00)	0.642 (1.00)	0.176 (1.00)	0.165 (1.00)	0.275 (1.00)	0.0739 (1.00)	0.596 (1.00)
Del Peak 10(6q15)	0 (0%)	64	0.12 (1.00)	0.148 (1.00)	0.401 (1.00)	0.112 (1.00)	0.279 (1.00)	0.156 (1.00)	0.441 (1.00)	0.0532 (1.00)
Del Peak 11(7q36 3)	0 (0%)	63	0.756 (1.00)	0.475 (1.00)	0.566 (1.00)	0.167 (1.00)	0.977 (1.00)	0.777 (1.00)	0.696 (1.00)	0.2 (1.00)
Del Peak 12(8p23 3)	0 (0%)	61	0.00493 (1.00)	0.00989 (1.00)	0.234 (1.00)	0.28 (1.00)	0.145 (1.00)	0.0083 (1.00)	0.19 (1.00)	0.208 (1.00)
Del Peak 15(9q34 3)	0 (0%)	58	0.0048 (1.00)	0.0416 (1.00)	0.199 (1.00)	0.521 (1.00)	0.248 (1.00)	0.256 (1.00)	0.406 (1.00)	0.135 (1.00)
Del Peak 16(10p15 3)	0 (0%)	44	0.0161 (1.00)	0.0482 (1.00)	0.124 (1.00)	0.416 (1.00)	0.505 (1.00)	0.245 (1.00)	0.606 (1.00)	0.269 (1.00)
Del Peak 18(11p15 5)	0 (0%)	45	0.0399 (1.00)	0.117 (1.00)	0.561 (1.00)	0.716 (1.00)	0.758 (1.00)	1 (1.00)	0.761 (1.00)	0.502 (1.00)
Del Peak 19(11q22 3)	0 (0%)	49	0.00179 (0.608)	0.0172 (1.00)	0.501 (1.00)	0.226 (1.00)	0.0833 (1.00)	0.172 (1.00)	0.0966 (1.00)	0.173 (1.00)
Del Peak 20(11q24 3)	0 (0%)	46	0.00477 (1.00)	0.00941 (1.00)	0.282 (1.00)	0.0768 (1.00)	0.132 (1.00)	0.0394 (1.00)	0.039 (1.00)	0.0572 (1.00)
Del Peak 21(12p13 1)	0 (0%)	58	0.0162 (1.00)	0.0499 (1.00)	0.402 (1.00)	0.725 (1.00)	0.323 (1.00)	0.215 (1.00)	0.419 (1.00)	0.103 (1.00)
Del Peak 23(14q24 1)	0 (0%)	48	0.0398 (1.00)	0.923 (1.00)	0.00135 (0.464)	0.542 (1.00)	0.189 (1.00)	0.204 (1.00)	0.275 (1.00)	0.262 (1.00)
Del Peak 24(16q12 1)	0 (0%)	37	0.0709 (1.00)	0.00198 (0.667)	0.349 (1.00)	0.187 (1.00)	0.0831 (1.00)	0.0394 (1.00)	0.107 (1.00)	0.0139 (1.00)
Del Peak 25(17p13 1)	0 (0%)	56	0.0725 (1.00)	0.023 (1.00)	0.0888 (1.00)	0.0369 (1.00)	0.132 (1.00)	0.0584 (1.00)	0.0616 (1.00)	0.0223 (1.00)
Del Peak 26(17q25 3)	0 (0%)	57	0.0327 (1.00)	0.109 (1.00)	0.445 (1.00)	0.0558 (1.00)	0.639 (1.00)	0.593 (1.00)	0.537 (1.00)	0.259 (1.00)
Del Peak 27(18p11 32)	0 (0%)	58	0.188 (1.00)	0.153 (1.00)	0.811 (1.00)	0.865 (1.00)	0.469 (1.00)	0.664 (1.00)	0.855 (1.00)	0.636 (1.00)
Del Peak 28(18q23)	0 (0%)	52	0.226 (1.00)	0.285 (1.00)	0.271 (1.00)	0.377 (1.00)	1 (1.00)	0.756 (1.00)	0.423 (1.00)	0.603 (1.00)
Del Peak 29(19p13 3)	0 (0%)	60	0.00489 (1.00)	0.00795 (1.00)	0.0856 (1.00)	0.0253 (1.00)	0.112 (1.00)	0.0348 (1.00)	0.0262 (1.00)	0.0694 (1.00)
Del Peak 31(21q22 3)	0 (0%)	56	0.468 (1.00)	0.838 (1.00)	0.423 (1.00)	0.647 (1.00)	0.756 (1.00)	0.677 (1.00)	0.462 (1.00)	1 (1.00)
Del Peak 33(Xp21 1)	0 (0%)	67	0.465 (1.00)	0.0711 (1.00)	0.636 (1.00)	0.317 (1.00)	0.0471 (1.00)	0.118 (1.00)	0.151 (1.00)	0.233 (1.00)
Del Peak 34(Xq21 1)	0 (0%)	48	0.52 (1.00)	0.132 (1.00)	0.279 (1.00)	0.0689 (1.00)	0.321 (1.00)	0.118 (1.00)	0.145 (1.00)	0.0568 (1.00)
Del Peak 35(Xq27 1)	0 (0%)	42	0.00258 (0.862)	0.0509 (1.00)	0.11 (1.00)	0.0461 (1.00)	0.631 (1.00)	0.456 (1.00)	0.211 (1.00)	0.185 (1.00)

'Amp Peak 1(1p32.1)' versus 'CN_CNMF'

P value = 0.000208 (Fisher's exact test), Q value = 0.075

Table S1. Gene #1: 'Amp Peak 1(1p32.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	22	18	19
AMP PEAK 1(1P32.1) CNV	5	10	12	1
AMP PEAK 1(1P32.1) WILD-TYPE	19	12	6	18

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p32.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(6p21.1)' versus 'METHLYATION_CNMF'

P value = 9.19e-05 (Fisher's exact test), Q value = 0.034

Table S2. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	27	30
AMP PEAK 4(6P21.1) CNV	6	14	1
AMP PEAK 4(6P21.1) WILD-TYPE	20	13	29

Figure S2. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 5(6q24.3)' versus 'METHLYATION_CNMF'

P value = 0.000521 (Fisher's exact test), Q value = 0.19

Table S3. Gene #5: 'Amp Peak 5(6q24.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	27	30
AMP PEAK 5(6Q24.3) CNV	15	9	3
AMP PEAK 5(6Q24.3) WILD-TYPE	11	18	27

Figure S3. Get High-res Image Gene #5: 'Amp Peak 5(6q24.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 5(6q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.17

Table S4. Gene #5: 'Amp Peak 5(6q24.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	37	43
AMP PEAK 5(6Q24.3) CNV	0	5	22
AMP PEAK 5(6Q24.3) WILD-TYPE	2	32	21

Figure S4. Get High-res Image Gene #5: 'Amp Peak 5(6q24.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(6q24.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.071

Table S5. Gene #5: 'Amp Peak 5(6q24.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	36	33
AMP PEAK 5(6Q24.3) CNV	8	16	3
AMP PEAK 5(6Q24.3) WILD-TYPE	5	20	30

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(6q24.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 9(12q15)' versus 'CN_CNMF'

P value = 3.02e-10 (Fisher's exact test), Q value = 1.2e-07

Table S6. Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	22	18	19
AMP PEAK 9(12Q15) CNV	12	22	4	2
AMP PEAK 9(12Q15) WILD-TYPE	12	0	14	17

Figure S6. Get High-res Image Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(12q15)' versus 'METHLYATION_CNMF'

P value = 5.12e-10 (Fisher's exact test), Q value = 1.9e-07

Table S7. Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	27	30
AMP PEAK 9(12Q15) CNV	19	20	1
AMP PEAK 9(12Q15) WILD-TYPE	7	7	29

Figure S7. Get High-res Image Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 9(12q15)' versus 'MRNASEQ_CNMF'

P value = 1.58e-08 (Chi-square test), Q value = 6e-06

Table S8. Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	11	16	2	17	15
AMP PEAK 9(12Q15) CNV	7	9	16	1	1	1
AMP PEAK 9(12Q15) WILD-TYPE	7	2	0	1	16	14

Figure S8. Get High-res Image Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 9(12q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.89e-10 (Fisher's exact test), Q value = 1.5e-07

Table S9. Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	31	43
AMP PEAK 9(12Q15) CNV	0	2	33
AMP PEAK 9(12Q15) WILD-TYPE	1	29	10

Figure S9. Get High-res Image Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(12q15)' versus 'MIRSEQ_CNMF'

P value = 8.35e-09 (Fisher's exact test), Q value = 3.2e-06

Table S10. Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	6	37	12	27
AMP PEAK 9(12Q15) CNV	5	27	6	1
AMP PEAK 9(12Q15) WILD-TYPE	1	10	6	26

Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Amp Peak 9(12q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.35e-08 (Fisher's exact test), Q value = 1.3e-05

Table S11. Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	37	43
AMP PEAK 9(12Q15) CNV	0	6	33
AMP PEAK 9(12Q15) WILD-TYPE	2	31	10

Figure S11. Get High-res Image Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 9(12q15)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.66e-12 (Fisher's exact test), Q value = 2.6e-09

Table S12. Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	36	33
AMP PEAK 9(12Q15) CNV	10	28	1
AMP PEAK 9(12Q15) WILD-TYPE	3	8	32

Figure S12. Get High-res Image Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 9(12q15)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.32e-09 (Fisher's exact test), Q value = 8.8e-07

Table S13. Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	41	40
AMP PEAK 9(12Q15) CNV	0	33	6
AMP PEAK 9(12Q15) WILD-TYPE	1	8	34

Figure S13. Get High-res Image Gene #9: 'Amp Peak 9(12q15)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 1(1p36.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000532 (Fisher's exact test), Q value = 0.19

Table S14. Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	31	43
DEL PEAK 1(1P36.32) CNV	1	17	7
DEL PEAK 1(1P36.32) WILD-TYPE	0	14	36

Figure S14. Get High-res Image Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_CNMF'

P value = 0.000306 (Fisher's exact test), Q value = 0.11

Table S15. Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	6	37	12	27
DEL PEAK 1(1P36.32) CNV	2	5	3	17
DEL PEAK 1(1P36.32) WILD-TYPE	4	32	9	10

Figure S15. Get High-res Image Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000215 (Fisher's exact test), Q value = 0.078

Table S16. Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	37	43
DEL PEAK 1(1P36.32) CNV	1	20	6
DEL PEAK 1(1P36.32) WILD-TYPE	1	17	37

Figure S16. Get High-res Image Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000668 (Fisher's exact test), Q value = 0.24

Table S17. Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	36	33
DEL PEAK 1(1P36.32) CNV	2	6	19
DEL PEAK 1(1P36.32) WILD-TYPE	11	30	14

Figure S17. Get High-res Image Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.27e-05 (Fisher's exact test), Q value = 0.027

Table S18. Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	41	40
DEL PEAK 1(1P36.32) CNV	1	5	21
DEL PEAK 1(1P36.32) WILD-TYPE	0	36	19

Figure S18. Get High-res Image Gene #14: 'Del Peak 1(1p36.32)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'CN_CNMF'

P value = 1.95e-05 (Fisher's exact test), Q value = 0.0073

Table S19. Gene #15: 'Del Peak 2(1p32.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	22	18	19
DEL PEAK 2(1P32.3) CNV	12	0	1	2
DEL PEAK 2(1P32.3) WILD-TYPE	12	22	17	17

Figure S19. Get High-res Image Gene #15: 'Del Peak 2(1p32.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(2q37.3)' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.04

Table S20. Gene #18: 'Del Peak 5(2q37.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	22	18	19
DEL PEAK 5(2Q37.3) CNV	12	6	15	3
DEL PEAK 5(2Q37.3) WILD-TYPE	12	16	3	16

Figure S20. Get High-res Image Gene #18: 'Del Peak 5(2q37.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(9p24.3)' versus 'CN_CNMF'

P value = 1.96e-06 (Fisher's exact test), Q value = 0.00073

Table S21. Gene #26: 'Del Peak 13(9p24.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	22	18	19
DEL PEAK 13(9P24.3) CNV	19	9	4	1
DEL PEAK 13(9P24.3) WILD-TYPE	5	13	14	18

Figure S21. Get High-res Image Gene #26: 'Del Peak 13(9p24.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(9p24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000499 (Fisher's exact test), Q value = 0.18

Table S22. Gene #26: 'Del Peak 13(9p24.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	31	43
DEL PEAK 13(9P24.3) CNV	1	6	26
DEL PEAK 13(9P24.3) WILD-TYPE	0	25	17

Figure S22. Get High-res Image Gene #26: 'Del Peak 13(9p24.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(9p21.3)' versus 'CN_CNMF'

P value = 1.33e-07 (Fisher's exact test), Q value = 5e-05

Table S23. Gene #27: 'Del Peak 14(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	22	18	19
DEL PEAK 14(9P21.3) CNV	22	8	4	3
DEL PEAK 14(9P21.3) WILD-TYPE	2	14	14	16

Figure S23. Get High-res Image Gene #27: 'Del Peak 14(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 0.000693 (Chi-square test), Q value = 0.24

Table S24. Gene #27: 'Del Peak 14(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	11	16	2	17	15
DEL PEAK 14(9P21.3) CNV	8	10	10	0	5	2
DEL PEAK 14(9P21.3) WILD-TYPE	6	1	6	2	12	13

Figure S24. Get High-res Image Gene #27: 'Del Peak 14(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 14(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.77e-05 (Fisher's exact test), Q value = 0.032

Table S25. Gene #27: 'Del Peak 14(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	31	43
DEL PEAK 14(9P21.3) CNV	1	6	28
DEL PEAK 14(9P21.3) WILD-TYPE	0	25	15

Figure S25. Get High-res Image Gene #27: 'Del Peak 14(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(9p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.97e-05 (Fisher's exact test), Q value = 0.033

Table S26. Gene #27: 'Del Peak 14(9p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	36	33
DEL PEAK 14(9P21.3) CNV	12	17	8
DEL PEAK 14(9P21.3) WILD-TYPE	1	19	25

Figure S26. Get High-res Image Gene #27: 'Del Peak 14(9p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 17(10q23.31)' versus 'CN_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.039

Table S27. Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	22	18	19
DEL PEAK 17(10Q23.31) CNV	13	3	15	10
DEL PEAK 17(10Q23.31) WILD-TYPE	11	19	3	9

Figure S27. Get High-res Image Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(10q23.31)' versus 'METHLYATION_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.079

Table S28. Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	27	30
DEL PEAK 17(10Q23.31) CNV	5	14	22
DEL PEAK 17(10Q23.31) WILD-TYPE	21	13	8

Figure S28. Get High-res Image Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 17(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000587 (Fisher's exact test), Q value = 0.21

Table S29. Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	31	43
DEL PEAK 17(10Q23.31) CNV	1	23	14
DEL PEAK 17(10Q23.31) WILD-TYPE	0	8	29

Figure S29. Get High-res Image Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(10q23.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000573 (Fisher's exact test), Q value = 0.2

Table S30. Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	41	40
DEL PEAK 17(10Q23.31) CNV	1	12	27
DEL PEAK 17(10Q23.31) WILD-TYPE	0	29	13

Figure S30. Get High-res Image Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 22(13q14.2)' versus 'CN_CNMF'

P value = 0.000194 (Fisher's exact test), Q value = 0.071

Table S31. Gene #35: 'Del Peak 22(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	22	18	19
DEL PEAK 22(13Q14.2) CNV	19	9	18	13
DEL PEAK 22(13Q14.2) WILD-TYPE	5	13	0	6

Figure S31. Get High-res Image Gene #35: 'Del Peak 22(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 22(13q14.2)' versus 'METHLYATION_CNMF'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.024

Table S32. Gene #35: 'Del Peak 22(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	27	30
DEL PEAK 22(13Q14.2) CNV	10	22	27
DEL PEAK 22(13Q14.2) WILD-TYPE	16	5	3

Figure S32. Get High-res Image Gene #35: 'Del Peak 22(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 30(19q13.33)' versus 'METHLYATION_CNMF'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.009

Table S33. Gene #43: 'Del Peak 30(19q13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	27	30
DEL PEAK 30(19Q13.33) CNV	1	16	13
DEL PEAK 30(19Q13.33) WILD-TYPE	25	11	17

Figure S33. Get High-res Image Gene #43: 'Del Peak 30(19q13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 32(22q13.32)' versus 'METHLYATION_CNMF'

P value = 0.000586 (Fisher's exact test), Q value = 0.21

Table S34. Gene #45: 'Del Peak 32(22q13.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	27	30
DEL PEAK 32(22Q13.32) CNV	4	18	12
DEL PEAK 32(22Q13.32) WILD-TYPE	22	9	18

Figure S34. Get High-res Image Gene #45: 'Del Peak 32(22q13.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = SARC-TP.transferedmergedcluster.txt
Number of patients = 83
Number of copy number variation regions = 48
Number of molecular subtypes = 8
Exclude regions 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] 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)

[4] GISTIC_version2

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