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

Sarcoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

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 (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16H4FWN

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 40 focal events and 8 molecular subtypes across 127 patients, 25 significant findings detected with P value < 0.05 and Q value < 0.25.

4p cnv correlated to 'CN_CNMF'.
10p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
10q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
13q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
16p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
16q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
17p cnv correlated to 'CN_CNMF'.
17q cnv correlated to 'CN_CNMF'.
18p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
18q cnv correlated to 'CN_CNMF'.
19p cnv correlated to 'CN_CNMF'.
19q cnv correlated to 'CN_CNMF'.
21q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
22q cnv correlated to 'CN_CNMF'.
xq cnv correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 40 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 25 significant findings detected.


		Clinical Features	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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
10q	72 (57%)	55	1.01e-06 (0.000323)	2.27e-05 (0.00709)	8.41e-06 (0.00266)	0.000247 (0.0755)	0.00557 (1.00)	0.00124 (0.357)	0.00565 (1.00)	0.000276 (0.0842)
10p	68 (54%)	59	1.23e-05 (0.00387)	0.000777 (0.23)	0.00223 (0.624)	0.0729 (1.00)	0.0349 (1.00)	0.0246 (1.00)	0.199 (1.00)	0.0147 (1.00)
13q	71 (56%)	56	4.44e-05 (0.0138)	0.000369 (0.112)	0.22 (1.00)	0.0576 (1.00)	0.508 (1.00)	0.561 (1.00)	0.622 (1.00)	0.514 (1.00)
16p	53 (42%)	74	0.000201 (0.0621)	0.000233 (0.0715)	0.515 (1.00)	0.171 (1.00)	0.139 (1.00)	0.806 (1.00)	0.838 (1.00)	0.467 (1.00)
16q	70 (55%)	57	0.000434 (0.13)	1.5e-06 (0.000477)	0.00136 (0.391)	0.00395 (1.00)	0.00105 (0.305)	0.00917 (1.00)	0.0254 (1.00)	0.00273 (0.753)
18p	50 (39%)	77	0.000759 (0.226)	0.00041 (0.124)	0.274 (1.00)	0.264 (1.00)	0.504 (1.00)	1 (1.00)	0.937 (1.00)	0.578 (1.00)
21q	55 (43%)	72	0.000615 (0.183)	1.55e-05 (0.00488)	0.0765 (1.00)	0.0243 (1.00)	0.245 (1.00)	0.493 (1.00)	0.0863 (1.00)	0.364 (1.00)
4p	46 (36%)	81	0.000227 (0.0699)	0.00179 (0.512)	0.073 (1.00)	0.269 (1.00)	0.385 (1.00)	1 (1.00)	0.642 (1.00)	1 (1.00)
17p	51 (40%)	76	0.00042 (0.126)	0.0025 (0.692)	0.223 (1.00)	0.357 (1.00)	0.15 (1.00)	1 (1.00)	0.181 (1.00)	0.39 (1.00)
17q	46 (36%)	81	7.24e-06 (0.0023)	0.0197 (1.00)	0.14 (1.00)	0.278 (1.00)	0.0216 (1.00)	0.327 (1.00)	0.436 (1.00)	0.0582 (1.00)
18q	50 (39%)	77	0.000538 (0.161)	0.00122 (0.354)	0.522 (1.00)	0.194 (1.00)	0.426 (1.00)	0.796 (1.00)	0.793 (1.00)	0.832 (1.00)
19p	45 (35%)	82	4.75e-08 (1.52e-05)	0.00726 (1.00)	0.312 (1.00)	0.272 (1.00)	0.479 (1.00)	0.573 (1.00)	0.84 (1.00)	0.725 (1.00)
19q	43 (34%)	84	1.96e-05 (0.00613)	0.015 (1.00)	0.7 (1.00)	0.367 (1.00)	0.525 (1.00)	0.509 (1.00)	0.79 (1.00)	0.811 (1.00)
22q	68 (54%)	59	0.000407 (0.123)	0.00221 (0.621)	0.24 (1.00)	0.101 (1.00)	0.081 (1.00)	0.507 (1.00)	0.637 (1.00)	0.364 (1.00)
xq	63 (50%)	64	0.00238 (0.661)	0.000148 (0.046)	0.103 (1.00)	0.000933 (0.274)	0.489 (1.00)	0.397 (1.00)	0.187 (1.00)	0.0875 (1.00)
1p	42 (33%)	85	0.00416 (1.00)	0.00326 (0.887)	0.0104 (1.00)	0.356 (1.00)	0.295 (1.00)	1 (1.00)	0.434 (1.00)	0.355 (1.00)
1q	43 (34%)	84	0.00504 (1.00)	0.0182 (1.00)	0.0395 (1.00)	0.085 (1.00)	0.332 (1.00)	0.401 (1.00)	0.357 (1.00)	0.166 (1.00)
2p	49 (39%)	78	0.00281 (0.772)	0.000964 (0.282)	0.00151 (0.433)	0.0186 (1.00)	0.0142 (1.00)	0.0847 (1.00)	0.231 (1.00)	0.0149 (1.00)
2q	38 (30%)	89	0.0087 (1.00)	0.114 (1.00)	0.772 (1.00)	0.321 (1.00)	0.309 (1.00)	1 (1.00)	0.796 (1.00)	0.372 (1.00)
3p	37 (29%)	90	0.0205 (1.00)	0.168 (1.00)	0.338 (1.00)	0.142 (1.00)	0.691 (1.00)	0.194 (1.00)	0.135 (1.00)	0.104 (1.00)
3q	41 (32%)	86	0.018 (1.00)	0.0177 (1.00)	0.258 (1.00)	0.0246 (1.00)	0.446 (1.00)	0.0546 (1.00)	0.0234 (1.00)	0.0526 (1.00)
4q	42 (33%)	85	0.00416 (1.00)	0.00664 (1.00)	0.223 (1.00)	0.441 (1.00)	0.302 (1.00)	1 (1.00)	0.91 (1.00)	1 (1.00)
5p	54 (43%)	73	0.0019 (0.54)	0.0415 (1.00)	0.549 (1.00)	0.572 (1.00)	0.44 (1.00)	0.614 (1.00)	0.0604 (1.00)	0.6 (1.00)
5q	49 (39%)	78	0.017 (1.00)	0.0499 (1.00)	1 (1.00)	0.574 (1.00)	0.392 (1.00)	0.642 (1.00)	0.106 (1.00)	0.832 (1.00)
6p	51 (40%)	76	0.354 (1.00)	0.145 (1.00)	1 (1.00)	1 (1.00)	0.668 (1.00)	0.644 (1.00)	0.716 (1.00)	0.841 (1.00)
6q	41 (32%)	86	0.0487 (1.00)	0.0443 (1.00)	0.951 (1.00)	0.27 (1.00)	0.791 (1.00)	0.671 (1.00)	0.414 (1.00)	0.728 (1.00)
7p	54 (43%)	73	0.0019 (0.54)	0.0543 (1.00)	0.131 (1.00)	0.25 (1.00)	0.917 (1.00)	1 (1.00)	0.806 (1.00)	0.531 (1.00)
7q	48 (38%)	79	0.00525 (1.00)	0.701 (1.00)	0.534 (1.00)	0.268 (1.00)	0.826 (1.00)	0.865 (1.00)	0.716 (1.00)	0.58 (1.00)
8p	53 (42%)	74	0.346 (1.00)	0.251 (1.00)	0.353 (1.00)	0.544 (1.00)	0.243 (1.00)	0.259 (1.00)	0.502 (1.00)	0.832 (1.00)
8q	49 (39%)	78	0.017 (1.00)	0.64 (1.00)	0.366 (1.00)	0.848 (1.00)	0.411 (1.00)	0.88 (1.00)	0.465 (1.00)	0.488 (1.00)
9p	63 (50%)	64	0.00315 (0.859)	0.00121 (0.352)	0.602 (1.00)	0.00218 (0.614)	0.000849 (0.25)	0.142 (1.00)	0.00687 (1.00)	0.151 (1.00)
9q	56 (44%)	71	0.00689 (1.00)	0.00287 (0.786)	0.758 (1.00)	0.00457 (1.00)	0.00556 (1.00)	0.119 (1.00)	0.00224 (0.626)	0.14 (1.00)
11p	53 (42%)	74	0.00466 (1.00)	0.00663 (1.00)	0.852 (1.00)	0.125 (1.00)	1 (1.00)	0.731 (1.00)	0.678 (1.00)	0.594 (1.00)
11q	47 (37%)	80	0.00203 (0.576)	0.018 (1.00)	0.747 (1.00)	0.111 (1.00)	0.479 (1.00)	0.327 (1.00)	0.198 (1.00)	0.257 (1.00)
12p	43 (34%)	84	0.0201 (1.00)	0.0882 (1.00)	0.935 (1.00)	0.137 (1.00)	0.0201 (1.00)	0.509 (1.00)	0.179 (1.00)	0.569 (1.00)
12q	36 (28%)	91	0.00482 (1.00)	0.0131 (1.00)	0.682 (1.00)	0.402 (1.00)	0.738 (1.00)	0.418 (1.00)	0.595 (1.00)	0.543 (1.00)
14q	61 (48%)	66	0.0859 (1.00)	0.0498 (1.00)	0.0996 (1.00)	0.159 (1.00)	0.648 (1.00)	1 (1.00)	0.558 (1.00)	1 (1.00)
15q	52 (41%)	75	0.00356 (0.964)	0.0596 (1.00)	0.668 (1.00)	0.754 (1.00)	0.389 (1.00)	0.806 (1.00)	0.837 (1.00)	0.467 (1.00)
20p	54 (43%)	73	0.0186 (1.00)	0.0157 (1.00)	0.187 (1.00)	0.168 (1.00)	0.663 (1.00)	0.878 (1.00)	0.663 (1.00)	1 (1.00)
20q	50 (39%)	77	0.0234 (1.00)	0.00857 (1.00)	0.609 (1.00)	0.0665 (1.00)	0.305 (1.00)	0.628 (1.00)	0.108 (1.00)	0.31 (1.00)

'4p' versus 'CN_CNMF'

P value = 0.000227 (Fisher's exact test), Q value = 0.07

Table S1. Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
4P MUTATED	7	31	8
4P WILD-TYPE	26	24	31

Figure S1. Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0039

Table S2. Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
10P MUTATED	9	42	17
10P WILD-TYPE	24	13	22

Figure S2. Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 0.000777 (Fisher's exact test), Q value = 0.23

Table S3. Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	43	50
10P MUTATED	9	29	30
10P WILD-TYPE	25	14	20

Figure S3. Get High-res Image Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q' versus 'CN_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00032

Table S4. Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
10Q MUTATED	8	44	20
10Q WILD-TYPE	25	11	19

Figure S4. Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.0071

Table S5. Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	43	50
10Q MUTATED	8	28	36
10Q WILD-TYPE	26	15	14

Figure S5. Get High-res Image Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 8.41e-06 (Fisher's exact test), Q value = 0.0027

Table S6. Gene #20: '10q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	30	32
10Q MUTATED	12	18	27
10Q WILD-TYPE	29	12	5

Figure S6. Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000247 (Fisher's exact test), Q value = 0.076

Table S7. Gene #20: '10q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	53	4
10Q MUTATED	35	21	1
10Q WILD-TYPE	11	32	3

Figure S7. Get High-res Image Gene #20: '10q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000276 (Fisher's exact test), Q value = 0.084

Table S8. Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	46	50
10Q MUTATED	1	16	36
10Q WILD-TYPE	0	30	14

Figure S8. Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q' versus 'CN_CNMF'

P value = 4.44e-05 (Fisher's exact test), Q value = 0.014

Table S9. Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
13Q MUTATED	13	43	15
13Q WILD-TYPE	20	12	24

Figure S9. Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 0.000369 (Fisher's exact test), Q value = 0.11

Table S10. Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	43	50
13Q MUTATED	10	32	29
13Q WILD-TYPE	24	11	21

Figure S10. Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p' versus 'CN_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.062

Table S11. Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
16P MUTATED	13	33	7
16P WILD-TYPE	20	22	32

Figure S11. Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'16p' versus 'METHLYATION_CNMF'

P value = 0.000233 (Fisher's exact test), Q value = 0.071

Table S12. Gene #28: '16p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	43	50
16P MUTATED	7	28	18
16P WILD-TYPE	27	15	32

Figure S12. Get High-res Image Gene #28: '16p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q' versus 'CN_CNMF'

P value = 0.000434 (Fisher's exact test), Q value = 0.13

Table S13. Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
16Q MUTATED	12	41	17
16Q WILD-TYPE	21	14	22

Figure S13. Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

'16q' versus 'METHLYATION_CNMF'

P value = 1.5e-06 (Fisher's exact test), Q value = 0.00048

Table S14. Gene #29: '16q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	43	50
16Q MUTATED	6	30	34
16Q WILD-TYPE	28	13	16

Figure S14. Get High-res Image Gene #29: '16q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.13

Table S15. Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
17P MUTATED	8	33	10
17P WILD-TYPE	25	22	29

Figure S15. Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17q' versus 'CN_CNMF'

P value = 7.24e-06 (Fisher's exact test), Q value = 0.0023

Table S16. Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
17Q MUTATED	6	33	7
17Q WILD-TYPE	27	22	32

Figure S16. Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'18p' versus 'CN_CNMF'

P value = 0.000759 (Fisher's exact test), Q value = 0.23

Table S17. Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
18P MUTATED	9	32	9
18P WILD-TYPE	24	23	30

Figure S17. Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.12

Table S18. Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	43	50
18P MUTATED	5	25	20
18P WILD-TYPE	29	18	30

Figure S18. Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q' versus 'CN_CNMF'

P value = 0.000538 (Fisher's exact test), Q value = 0.16

Table S19. Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
18Q MUTATED	10	32	8
18Q WILD-TYPE	23	23	31

Figure S19. Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'19p' versus 'CN_CNMF'

P value = 4.75e-08 (Fisher's exact test), Q value = 1.5e-05

Table S20. Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
19P MUTATED	10	33	2
19P WILD-TYPE	23	22	37

Figure S20. Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'CN_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0061

Table S21. Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
19Q MUTATED	9	30	4
19Q WILD-TYPE	24	25	35

Figure S21. Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'21q' versus 'CN_CNMF'

P value = 0.000615 (Fisher's exact test), Q value = 0.18

Table S22. Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
21Q MUTATED	14	33	8
21Q WILD-TYPE	19	22	31

Figure S22. Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

'21q' versus 'METHLYATION_CNMF'

P value = 1.55e-05 (Fisher's exact test), Q value = 0.0049

Table S23. Gene #38: '21q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	43	50
21Q MUTATED	9	31	15
21Q WILD-TYPE	25	12	35

Figure S23. Get High-res Image Gene #38: '21q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q' versus 'CN_CNMF'

P value = 0.000407 (Fisher's exact test), Q value = 0.12

Table S24. Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	55	39
22Q MUTATED	15	40	13
22Q WILD-TYPE	18	15	26

Figure S24. Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.046

Table S25. Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	43	50
XQ MUTATED	7	23	33
XQ WILD-TYPE	27	20	17

Figure S25. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = SARC-TP.transferedmergedcluster.txt
Number of patients = 127
Number of significantly focal cnvs = 40
Number of molecular subtypes = 8
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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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