Correlation between copy number variation genes and molecular subtypes

Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1MC8X2J

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 20 peak regions and 6 molecular subtypes across 191 patients, 35 significant findings detected with Q value < 0.25.

Amp Peak 1(1p33) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(11q23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 4(13q31.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(20q11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(21q22.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 2(3p13) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 4(5q31.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 5(7p12.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 6(7q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 7(7q34) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 10(12p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 12(16q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 13(17p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 14(17q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 15(18p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 16(20q13.13) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 20 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 35 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Chi-square test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 5(7p12 1)	0 (0%)	175	2.4e-07 (2.64e-05)	0.000667 (0.064)	0.00179 (0.155)	0.00272 (0.225)	0.00595 (0.452)	0.00176 (0.155)
Del Peak 4(5q31 2)	0 (0%)	173	6.32e-15 (7.27e-13)	6.11e-05 (0.00623)	0.0053 (0.413)	0.0923 (1.00)	0.000809 (0.0769)	0.00042 (0.0407)
Del Peak 6(7q32 3)	0 (0%)	168	8.78e-07 (9.31e-05)	0.000189 (0.0186)	0.0384 (1.00)	0.022 (1.00)	0.00255 (0.214)	9.87e-05 (0.00977)
Del Peak 7(7q34)	0 (0%)	167	2.83e-06 (0.000298)	7.4e-05 (0.00748)	0.0221 (1.00)	0.0212 (1.00)	0.000836 (0.0786)	1.55e-05 (0.00161)
Amp Peak 6(21q22 2)	0 (0%)	177	9.35e-32 (1.08e-29)	0.00156 (0.14)	0.00336 (0.276)	0.337 (1.00)	0.00177 (0.155)	0.0173 (1.00)
Del Peak 13(17p13 2)	0 (0%)	176	1.68e-14 (1.91e-12)	0.00105 (0.0981)	0.0113 (0.765)	0.0211 (1.00)	0.0874 (1.00)	0.00133 (0.123)
Amp Peak 3(11q23 3)	0 (0%)	174	4.87e-33 (5.7e-31)	8.51e-05 (0.00851)	0.373 (1.00)	0.784 (1.00)	0.746 (1.00)	0.945 (1.00)
Del Peak 2(3p13)	0 (0%)	182	0.00179 (0.155)	0.137 (1.00)	0.0349 (1.00)	0.718 (1.00)	0.012 (0.806)	0.00166 (0.147)
Amp Peak 1(1p33)	0 (0%)	184	4.86e-07 (5.2e-05)	0.00516 (0.413)	0.124 (1.00)	0.665 (1.00)	0.00989 (0.682)	0.23 (1.00)
Amp Peak 4(13q31 3)	0 (0%)	184	1.96e-10 (2.2e-08)	0.00516 (0.413)	0.0668 (1.00)	0.0965 (1.00)	0.735 (1.00)	0.143 (1.00)
Amp Peak 5(20q11 21)	0 (0%)	188	0.00135 (0.123)	0.185 (1.00)		0.55 (1.00)
Del Peak 10(12p13 2)	0 (0%)	181	8.25e-13 (9.33e-11)	0.00776 (0.566)	0.197 (1.00)	0.167 (1.00)	0.0682 (1.00)	0.0217 (1.00)
Del Peak 12(16q23 1)	0 (0%)	182	2.61e-07 (2.84e-05)	0.0648 (1.00)	0.332 (1.00)	1 (1.00)	0.0442 (1.00)	0.0493 (1.00)
Del Peak 14(17q11 2)	0 (0%)	178	1.72e-05 (0.00177)	0.029 (1.00)	0.156 (1.00)	0.222 (1.00)	0.136 (1.00)	0.00838 (0.595)
Del Peak 15(18p11 21)	0 (0%)	182	4.63e-07 (5e-05)	0.00832 (0.595)	0.381 (1.00)	0.718 (1.00)	0.213 (1.00)	0.0914 (1.00)
Del Peak 16(20q13 13)	0 (0%)	187	9.73e-10 (1.08e-07)	0.0808 (1.00)	0.786 (1.00)	1 (1.00)	0.125 (1.00)	0.222 (1.00)
Amp Peak 2(1q43)	0 (0%)	184	0.0063 (0.473)	0.00516 (0.413)	0.373 (1.00)	0.425 (1.00)	0.137 (1.00)	0.121 (1.00)
Del Peak 3(3q26 31)	0 (0%)	188	0.00355 (0.287)	0.185 (1.00)	0.786 (1.00)	1 (1.00)	0.0618 (1.00)	0.0481 (1.00)
Del Peak 9(9q21 32)	0 (0%)	186	0.63 (1.00)	0.416 (1.00)	0.176 (1.00)	0.664 (1.00)	0.183 (1.00)	0.108 (1.00)
Del Peak 11(12q21 33)	0 (0%)	188	0.057 (1.00)	0.38 (1.00)	0.186 (1.00)	0.552 (1.00)	0.00827 (0.595)	0.00696 (0.515)

'Amp Peak 1(1p33)' versus 'CN_CNMF'

P value = 4.86e-07 (Chi-square test), Q value = 5.2e-05

Table S1. Gene #1: 'Amp Peak 1(1p33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 1(1P33) CNV	0	3	0	4	0
AMP PEAK 1(1P33) WILD-TYPE	142	12	15	14	1

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(11q23.3)' versus 'CN_CNMF'

P value = 4.87e-33 (Chi-square test), Q value = 5.7e-31

Table S2. Gene #3: 'Amp Peak 3(11q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 3(11Q23.3) CNV	0	14	0	2	1
AMP PEAK 3(11Q23.3) WILD-TYPE	142	1	15	16	0

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(11q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(11q23.3)' versus 'METHLYATION_CNMF'

P value = 8.51e-05 (Chi-square test), Q value = 0.0085

Table S3. Gene #3: 'Amp Peak 3(11q23.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
AMP PEAK 3(11Q23.3) CNV	0	0	12	4	1
AMP PEAK 3(11Q23.3) WILD-TYPE	46	44	49	10	19

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(11q23.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(13q31.3)' versus 'CN_CNMF'

P value = 1.96e-10 (Chi-square test), Q value = 2.2e-08

Table S4. Gene #4: 'Amp Peak 4(13q31.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 4(13Q31.3) CNV	0	1	0	6	0
AMP PEAK 4(13Q31.3) WILD-TYPE	142	14	15	12	1

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(13q31.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(20q11.21)' versus 'CN_CNMF'

P value = 0.00135 (Chi-square test), Q value = 0.12

Table S5. Gene #5: 'Amp Peak 5(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 5(20Q11.21) CNV	0	0	2	1	0
AMP PEAK 5(20Q11.21) WILD-TYPE	142	15	13	17	1

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(21q22.2)' versus 'CN_CNMF'

P value = 9.35e-32 (Chi-square test), Q value = 1.1e-29

Table S6. Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 6(21Q22.2) CNV	0	0	13	1	0
AMP PEAK 6(21Q22.2) WILD-TYPE	142	15	2	17	1

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(21q22.2)' versus 'METHLYATION_CNMF'

P value = 0.00156 (Chi-square test), Q value = 0.14

Table S7. Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
AMP PEAK 6(21Q22.2) CNV	1	0	11	0	1
AMP PEAK 6(21Q22.2) WILD-TYPE	45	44	50	14	19

Figure S7. Get High-res Image Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 6(21q22.2)' versus 'MIRSEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.15

Table S8. Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	37	41	43
AMP PEAK 6(21Q22.2) CNV	1	4	7	0
AMP PEAK 6(21Q22.2) WILD-TYPE	57	33	34	43

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 2(3p13)' versus 'CN_CNMF'

P value = 0.00179 (Chi-square test), Q value = 0.15

Table S9. Gene #7: 'Del Peak 2(3p13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 2(3P13) CNV	2	1	3	3	0
DEL PEAK 2(3P13) WILD-TYPE	140	14	12	15	1

Figure S9. Get High-res Image Gene #7: 'Del Peak 2(3p13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(3p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.15

Table S10. Gene #7: 'Del Peak 2(3p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	79	65
DEL PEAK 2(3P13) CNV	5	0	3
DEL PEAK 2(3P13) WILD-TYPE	30	79	62

Figure S10. Get High-res Image Gene #7: 'Del Peak 2(3p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(5q31.2)' versus 'CN_CNMF'

P value = 6.32e-15 (Chi-square test), Q value = 7.3e-13

Table S11. Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 4(5Q31.2) CNV	1	1	7	8	1
DEL PEAK 4(5Q31.2) WILD-TYPE	141	14	8	10	0

Figure S11. Get High-res Image Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 4(5q31.2)' versus 'METHLYATION_CNMF'

P value = 6.11e-05 (Chi-square test), Q value = 0.0062

Table S12. Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 4(5Q31.2) CNV	1	0	15	0	2
DEL PEAK 4(5Q31.2) WILD-TYPE	45	44	46	14	18

Figure S12. Get High-res Image Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 4(5q31.2)' versus 'MIRSEQ_CNMF'

P value = 0.000809 (Fisher's exact test), Q value = 0.077

Table S13. Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	37	41	43
DEL PEAK 4(5Q31.2) CNV	1	10	3	3
DEL PEAK 4(5Q31.2) WILD-TYPE	57	27	38	40

Figure S13. Get High-res Image Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 4(5q31.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.041

Table S14. Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	79	65
DEL PEAK 4(5Q31.2) CNV	10	3	4
DEL PEAK 4(5Q31.2) WILD-TYPE	25	76	61

Figure S14. Get High-res Image Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(7p12.1)' versus 'CN_CNMF'

P value = 2.4e-07 (Chi-square test), Q value = 2.6e-05

Table S15. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 5(7P12.1) CNV	7	1	0	7	1
DEL PEAK 5(7P12.1) WILD-TYPE	135	14	15	11	0

Figure S15. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(7p12.1)' versus 'METHLYATION_CNMF'

P value = 0.000667 (Chi-square test), Q value = 0.064

Table S16. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 5(7P12.1) CNV	1	0	13	1	1
DEL PEAK 5(7P12.1) WILD-TYPE	45	44	48	13	19

Figure S16. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 5(7p12.1)' versus 'MRNASEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.15

Table S17. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	52	44
DEL PEAK 5(7P12.1) CNV	12	0	3
DEL PEAK 5(7P12.1) WILD-TYPE	58	52	41

Figure S17. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 5(7p12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.23

Table S18. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	110	56
DEL PEAK 5(7P12.1) CNV	15	0
DEL PEAK 5(7P12.1) WILD-TYPE	95	56

Figure S18. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(7p12.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.15

Table S19. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	79	65
DEL PEAK 5(7P12.1) CNV	9	3	4
DEL PEAK 5(7P12.1) WILD-TYPE	26	76	61

Figure S19. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(7q32.3)' versus 'CN_CNMF'

P value = 8.78e-07 (Chi-square test), Q value = 9.3e-05

Table S20. Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 6(7Q32.3) CNV	7	3	5	7	1
DEL PEAK 6(7Q32.3) WILD-TYPE	135	12	10	11	0

Figure S20. Get High-res Image Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(7q32.3)' versus 'METHLYATION_CNMF'

P value = 0.000189 (Chi-square test), Q value = 0.019

Table S21. Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 6(7Q32.3) CNV	1	1	17	2	2
DEL PEAK 6(7Q32.3) WILD-TYPE	45	43	44	12	18

Figure S21. Get High-res Image Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 6(7q32.3)' versus 'MIRSEQ_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.21

Table S22. Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	37	41	43
DEL PEAK 6(7Q32.3) CNV	2	11	5	4
DEL PEAK 6(7Q32.3) WILD-TYPE	56	26	36	39

Figure S22. Get High-res Image Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 6(7q32.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.87e-05 (Fisher's exact test), Q value = 0.0098

Table S23. Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	79	65
DEL PEAK 6(7Q32.3) CNV	12	3	7
DEL PEAK 6(7Q32.3) WILD-TYPE	23	76	58

Figure S23. Get High-res Image Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(7q34)' versus 'CN_CNMF'

P value = 2.83e-06 (Chi-square test), Q value = 3e-04

Table S24. Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 7(7Q34) CNV	8	3	5	7	1
DEL PEAK 7(7Q34) WILD-TYPE	134	12	10	11	0

Figure S24. Get High-res Image Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(7q34)' versus 'METHLYATION_CNMF'

P value = 7.4e-05 (Chi-square test), Q value = 0.0075

Table S25. Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 7(7Q34) CNV	1	1	18	2	2
DEL PEAK 7(7Q34) WILD-TYPE	45	43	43	12	18

Figure S25. Get High-res Image Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(7q34)' versus 'MIRSEQ_CNMF'

P value = 0.000836 (Fisher's exact test), Q value = 0.079

Table S26. Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	37	41	43
DEL PEAK 7(7Q34) CNV	2	12	5	4
DEL PEAK 7(7Q34) WILD-TYPE	56	25	36	39

Figure S26. Get High-res Image Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 7(7q34)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.55e-05 (Fisher's exact test), Q value = 0.0016

Table S27. Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	79	65
DEL PEAK 7(7Q34) CNV	13	3	7
DEL PEAK 7(7Q34) WILD-TYPE	22	76	58

Figure S27. Get High-res Image Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(12p13.2)' versus 'CN_CNMF'

P value = 8.25e-13 (Chi-square test), Q value = 9.3e-11

Table S28. Gene #14: 'Del Peak 10(12p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 10(12P13.2) CNV	1	1	0	8	0
DEL PEAK 10(12P13.2) WILD-TYPE	141	14	15	10	1

Figure S28. Get High-res Image Gene #14: 'Del Peak 10(12p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(16q23.1)' versus 'CN_CNMF'

P value = 2.61e-07 (Chi-square test), Q value = 2.8e-05

Table S29. Gene #16: 'Del Peak 12(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 12(16Q23.1) CNV	2	1	1	4	1
DEL PEAK 12(16Q23.1) WILD-TYPE	140	14	14	14	0

Figure S29. Get High-res Image Gene #16: 'Del Peak 12(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(17p13.2)' versus 'CN_CNMF'

P value = 1.68e-14 (Chi-square test), Q value = 1.9e-12

Table S30. Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 13(17P13.2) CNV	0	1	5	8	1
DEL PEAK 13(17P13.2) WILD-TYPE	142	14	10	10	0

Figure S30. Get High-res Image Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(17p13.2)' versus 'METHLYATION_CNMF'

P value = 0.00105 (Chi-square test), Q value = 0.098

Table S31. Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 13(17P13.2) CNV	0	1	12	0	2
DEL PEAK 13(17P13.2) WILD-TYPE	46	43	49	14	18

Figure S31. Get High-res Image Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 13(17p13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.12

Table S32. Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	79	65
DEL PEAK 13(17P13.2) CNV	7	1	7
DEL PEAK 13(17P13.2) WILD-TYPE	28	78	58

Figure S32. Get High-res Image Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(17q11.2)' versus 'CN_CNMF'

P value = 1.72e-05 (Chi-square test), Q value = 0.0018

Table S33. Gene #18: 'Del Peak 14(17q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 14(17Q11.2) CNV	2	3	3	5	0
DEL PEAK 14(17Q11.2) WILD-TYPE	140	12	12	13	1

Figure S33. Get High-res Image Gene #18: 'Del Peak 14(17q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(18p11.21)' versus 'CN_CNMF'

P value = 4.63e-07 (Chi-square test), Q value = 5e-05

Table S34. Gene #19: 'Del Peak 15(18p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 15(18P11.21) CNV	1	0	3	5	0
DEL PEAK 15(18P11.21) WILD-TYPE	141	15	12	13	1

Figure S34. Get High-res Image Gene #19: 'Del Peak 15(18p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(20q13.13)' versus 'CN_CNMF'

P value = 9.73e-10 (Chi-square test), Q value = 1.1e-07

Table S35. Gene #20: 'Del Peak 16(20q13.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 16(20Q13.13) CNV	0	0	4	0	0
DEL PEAK 16(20Q13.13) WILD-TYPE	142	15	11	18	1

Figure S35. Get High-res Image Gene #20: 'Del Peak 16(20q13.13)' versus Molecular Subtype #1: 'CN_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 = LAML-TB.transferedmergedcluster.txt
Number of patients = 191
Number of copy number variation regions = 20
Number of molecular subtypes = 6
Exclude regions that fewer than K tumors have alterations, K = 3

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

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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] 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)

[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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