Correlation between copy number variation genes (focal) and selected clinical features

Thyroid Adenocarcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

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 (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1FX77PX

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 24 arm-level results and 15 clinical features across 284 patients, 15 significant findings detected with Q value < 0.25.

Del Peak 2(2p22.3) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Del Peak 3(2q35) cnv correlated to 'HISTOLOGICAL.TYPE', 'NUMBER.OF.LYMPH.NODES', and 'NEOPLASM.DISEASESTAGE'.
Del Peak 10(8q24.22) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Del Peak 11(9p21.3) cnv correlated to 'NEOPLASM.DISEASESTAGE'.
Del Peak 12(9q22.32) cnv correlated to 'NEOPLASM.DISEASESTAGE'.
Del Peak 15(11p15.1) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Del Peak 16(13q12.3) cnv correlated to 'RADIATIONEXPOSURE'.
Del Peak 17(13q14.3) cnv correlated to 'RADIATIONEXPOSURE'.
Del Peak 18(15q25.3) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Del Peak 26(21q21.1) cnv correlated to 'NEOPLASM.DISEASESTAGE'.
Del Peak 30(Xq22.1) cnv correlated to 'NEOPLASM.DISEASESTAGE'.
Del Peak 31(Xq22.3) cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 24 arm-level results and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	RADIATIONEXPOSURE	DISTANT METASTASIS	EXTRATHYROIDAL EXTENSION	LYMPH NODE METASTASIS	COMPLETENESS OF RESECTION	NUMBER OF LYMPH NODES	TUMOR STAGECODE	NEOPLASM DISEASESTAGE	MULTIFOCALITY	TUMOR SIZE
	nCNV (%)	nWild-Type	logrank test	t-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	Chi-square test	Fisher's exact test	t-test	t-test	Chi-square test	Fisher's exact test	t-test
Del Peak 3(2q35)	8 (3%)	276	1 (1.00)	0.0123 (1.00)	0.684 (1.00)	0.000323 (0.104)	1 (1.00)	1 (1.00)	0.382 (1.00)	0.729 (1.00)	0.182 (1.00)	0.25 (1.00)	2.91e-14 (9.67e-12)		0.00014 (0.0453)	1 (1.00)	0.185 (1.00)
Del Peak 31(Xq22 3)	4 (1%)	280	1 (1.00)	0.0642 (1.00)	0.0536 (1.00)	0.206 (1.00)	1 (1.00)	0.128 (1.00)	0.18 (1.00)	0.606 (1.00)	0.36 (1.00)	0.494 (1.00)	3.02e-14 (1e-11)		2.08e-06 (0.000679)	1 (1.00)	0.515 (1.00)
Del Peak 2(2p22 3)	9 (3%)	275	1 (1.00)	0.157 (1.00)	0.455 (1.00)	0.019 (1.00)	1 (1.00)	1 (1.00)	0.391 (1.00)	0.258 (1.00)	0.135 (1.00)	0.788 (1.00)	2.86e-14 (9.52e-12)		0.00102 (0.325)	0.749 (1.00)	0.688 (1.00)
Del Peak 10(8q24 22)	5 (2%)	279	1 (1.00)	0.0567 (1.00)	0.109 (1.00)	0.0294 (1.00)	1 (1.00)	1 (1.00)	0.682 (1.00)	1 (1.00)	0.464 (1.00)	0.575 (1.00)	3.08e-14 (1.01e-11)		0.00506 (1.00)	0.684 (1.00)	0.185 (1.00)
Del Peak 11(9p21 3)	7 (2%)	277	1 (1.00)	0.0401 (1.00)	0.682 (1.00)	0.627 (1.00)	1 (1.00)	1 (1.00)	0.519 (1.00)	0.3 (1.00)	0.309 (1.00)	0.309 (1.00)	0.00238 (0.755)		1.88e-05 (0.00612)	0.282 (1.00)	0.124 (1.00)
Del Peak 12(9q22 32)	10 (4%)	274	1 (1.00)	0.124 (1.00)	1 (1.00)	0.239 (1.00)	0.402 (1.00)	0.34 (1.00)	0.302 (1.00)	0.553 (1.00)	0.101 (1.00)	0.822 (1.00)	0.373 (1.00)		8.59e-05 (0.0279)	1 (1.00)	0.833 (1.00)
Del Peak 15(11p15 1)	4 (1%)	280	0.00468 (1.00)	0.031 (1.00)	0.273 (1.00)	0.145 (1.00)	0.184 (1.00)	1 (1.00)	0.18 (1.00)	0.606 (1.00)	0.36 (1.00)	0.494 (1.00)	3.02e-14 (1e-11)		0.515 (1.00)	0.622 (1.00)	0.238 (1.00)
Del Peak 16(13q12 3)	10 (4%)	274	0.00468 (1.00)	0.0131 (1.00)	0.131 (1.00)	0.108 (1.00)	0.402 (1.00)	0.000241 (0.0777)	0.302 (1.00)	0.553 (1.00)	0.277 (1.00)	0.488 (1.00)	0.0311 (1.00)		0.118 (1.00)	0.749 (1.00)	0.137 (1.00)
Del Peak 17(13q14 3)	13 (5%)	271	0.00468 (1.00)	0.177 (1.00)	0.33 (1.00)	0.162 (1.00)	0.129 (1.00)	0.000601 (0.192)	0.441 (1.00)	0.446 (1.00)	0.0996 (1.00)	1 (1.00)	0.0358 (1.00)		0.535 (1.00)	0.377 (1.00)	0.353 (1.00)
Del Peak 18(15q25 3)	4 (1%)	280	1 (1.00)	0.247 (1.00)	0.575 (1.00)	0.145 (1.00)	1 (1.00)	1 (1.00)	0.18 (1.00)	1 (1.00)	0.36 (1.00)	0.494 (1.00)	3.02e-14 (1e-11)		0.0489 (1.00)	0.622 (1.00)	0.626 (1.00)
Del Peak 26(21q21 1)	7 (2%)	277	1 (1.00)	0.0042 (1.00)	1 (1.00)	0.447 (1.00)	1 (1.00)	1 (1.00)	0.519 (1.00)	1 (1.00)	0.334 (1.00)	0.201 (1.00)	0.946 (1.00)		0.000339 (0.109)	1 (1.00)	0.73 (1.00)
Del Peak 30(Xq22 1)	6 (2%)	278	1 (1.00)	0.177 (1.00)	0.0397 (1.00)	0.135 (1.00)	1 (1.00)	0.204 (1.00)	0.295 (1.00)	0.411 (1.00)	0.382 (1.00)	0.246 (1.00)	0.691 (1.00)		0.000772 (0.246)	0.684 (1.00)	0.682 (1.00)
Del Peak 5(6q22 31)	4 (1%)	280	0.00468 (1.00)	0.197 (1.00)	1 (1.00)	0.802 (1.00)	0.184 (1.00)	1 (1.00)	0.18 (1.00)	0.606 (1.00)	0.769 (1.00)	1 (1.00)	0.00663 (1.00)		0.0718 (1.00)	0.37 (1.00)	0.033 (1.00)
Del Peak 6(6q27)	4 (1%)	280	0.00468 (1.00)	0.197 (1.00)	1 (1.00)	0.802 (1.00)	0.184 (1.00)	1 (1.00)	0.18 (1.00)	0.606 (1.00)	0.769 (1.00)	1 (1.00)	0.00663 (1.00)		0.0718 (1.00)	0.37 (1.00)	0.033 (1.00)
Del Peak 8(7q34)	4 (1%)	280	1 (1.00)	0.759 (1.00)	1 (1.00)	0.251 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.606 (1.00)	0.769 (1.00)	1 (1.00)	0.374 (1.00)		0.7 (1.00)	0.37 (1.00)	0.23 (1.00)
Del Peak 13(10q21 2)	7 (2%)	277	1 (1.00)	0.565 (1.00)	1 (1.00)	0.0672 (1.00)	0.301 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.585 (1.00)	0.699 (1.00)	0.293 (1.00)		0.618 (1.00)	1 (1.00)	0.0236 (1.00)
Del Peak 14(10q23 31)	8 (3%)	276	1 (1.00)	0.0207 (1.00)	0.428 (1.00)	0.0242 (1.00)	1 (1.00)	1 (1.00)	0.765 (1.00)	0.729 (1.00)	0.219 (1.00)	1 (1.00)	0.0584 (1.00)		0.0117 (1.00)	0.723 (1.00)	0.0374 (1.00)
Del Peak 20(16q23 3)	3 (1%)	281	1 (1.00)	0.323 (1.00)	0.572 (1.00)	0.0221 (1.00)	1 (1.00)	0.128 (1.00)	1 (1.00)	0.192 (1.00)	0.708 (1.00)	0.4 (1.00)	0.0561 (1.00)		0.139 (1.00)	1 (1.00)
Del Peak 21(17p13 1)	5 (2%)	279	1 (1.00)	0.944 (1.00)	0.333 (1.00)	0.367 (1.00)	0.0208 (1.00)	1 (1.00)	0.429 (1.00)	0.102 (1.00)	0.215 (1.00)	1 (1.00)	0.293 (1.00)		0.211 (1.00)	0.214 (1.00)	0.306 (1.00)
Del Peak 22(18p11 21)	3 (1%)	281	1 (1.00)	0.958 (1.00)	0.572 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.865 (1.00)	1 (1.00)	0.0561 (1.00)		0.0502 (1.00)	0.622 (1.00)	0.976 (1.00)
Del Peak 23(19p13 2)	4 (1%)	280	1 (1.00)	0.0248 (1.00)	1 (1.00)	0.145 (1.00)	1 (1.00)	1 (1.00)	0.604 (1.00)	1 (1.00)	0.105 (1.00)	0.4 (1.00)			0.722 (1.00)	0.37 (1.00)
Del Peak 27(22q13 31)	49 (17%)	235	0.724 (1.00)	0.748 (1.00)	0.719 (1.00)	0.0552 (1.00)	0.477 (1.00)	0.695 (1.00)	0.63 (1.00)	0.509 (1.00)	0.644 (1.00)	0.4 (1.00)	0.684 (1.00)		0.854 (1.00)	0.109 (1.00)	0.305 (1.00)
Del Peak 28(22q13 2)	49 (17%)	235	0.724 (1.00)	0.748 (1.00)	0.719 (1.00)	0.0552 (1.00)	0.477 (1.00)	0.695 (1.00)	0.63 (1.00)	0.509 (1.00)	0.644 (1.00)	0.4 (1.00)	0.684 (1.00)		0.854 (1.00)	0.109 (1.00)	0.305 (1.00)
Del Peak 29(22q13 32)	50 (18%)	234	0.724 (1.00)	0.798 (1.00)	0.595 (1.00)	0.0314 (1.00)	0.476 (1.00)	0.695 (1.00)	0.722 (1.00)	0.509 (1.00)	0.587 (1.00)	0.4 (1.00)	0.607 (1.00)		0.882 (1.00)	0.0799 (1.00)	0.305 (1.00)

'Del Peak 2(2p22.3) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.86e-14 (t-test), Q value = 9.5e-12

Table S1. Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	225	2.8 (5.2)
DEL PEAK 2(2P22.3) MUTATED	7	0.0 (0.0)
DEL PEAK 2(2P22.3) WILD-TYPE	218	2.9 (5.3)

Figure S1. Get High-res Image Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 3(2q35) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000323 (Fisher's exact test), Q value = 0.1

Table S2. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	OTHER	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	18	167	69	30
DEL PEAK 3(2Q35) MUTATED	4	1	3	0
DEL PEAK 3(2Q35) WILD-TYPE	14	166	66	30

Figure S2. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 3(2q35) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.91e-14 (t-test), Q value = 9.7e-12

Table S3. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	225	2.8 (5.2)
DEL PEAK 3(2Q35) MUTATED	6	0.0 (0.0)
DEL PEAK 3(2Q35) WILD-TYPE	219	2.9 (5.3)

Figure S3. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 3(2q35) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00014 (Chi-square test), Q value = 0.045

Table S4. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	161	32	62	25	3
DEL PEAK 3(2Q35) MUTATED	1	5	2	0	0
DEL PEAK 3(2Q35) WILD-TYPE	160	27	60	25	3

Figure S4. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 10(8q24.22) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.08e-14 (t-test), Q value = 1e-11

Table S5. Gene #6: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	225	2.8 (5.2)
DEL PEAK 10(8Q24.22) MUTATED	3	0.0 (0.0)
DEL PEAK 10(8Q24.22) WILD-TYPE	222	2.9 (5.3)

Figure S5. Get High-res Image Gene #6: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 11(9p21.3) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.88e-05 (Chi-square test), Q value = 0.0061

Table S6. Gene #7: 'Del Peak 11(9p21.3) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	161	32	62	25	3
DEL PEAK 11(9P21.3) MUTATED	1	5	0	1	0
DEL PEAK 11(9P21.3) WILD-TYPE	160	27	62	24	3

Figure S6. Get High-res Image Gene #7: 'Del Peak 11(9p21.3) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 12(9q22.32) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.59e-05 (Chi-square test), Q value = 0.028

Table S7. Gene #8: 'Del Peak 12(9q22.32) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	161	32	62	25	3
DEL PEAK 12(9Q22.32) MUTATED	2	5	0	3	0
DEL PEAK 12(9Q22.32) WILD-TYPE	159	27	62	22	3

Figure S7. Get High-res Image Gene #8: 'Del Peak 12(9q22.32) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 15(11p15.1) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.02e-14 (t-test), Q value = 1e-11

Table S8. Gene #11: 'Del Peak 15(11p15.1) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	225	2.8 (5.2)
DEL PEAK 15(11P15.1) MUTATED	4	0.0 (0.0)
DEL PEAK 15(11P15.1) WILD-TYPE	221	2.9 (5.3)

Figure S8. Get High-res Image Gene #11: 'Del Peak 15(11p15.1) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 16(13q12.3) mutation analysis' versus 'RADIATIONEXPOSURE'

P value = 0.000241 (Fisher's exact test), Q value = 0.078

Table S9. Gene #12: 'Del Peak 16(13q12.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONEXPOSURE'

nPatients	NO	YES
ALL	237	11
DEL PEAK 16(13Q12.3) MUTATED	5	4
DEL PEAK 16(13Q12.3) WILD-TYPE	232	7

Figure S9. Get High-res Image Gene #12: 'Del Peak 16(13q12.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONEXPOSURE'

'Del Peak 17(13q14.3) mutation analysis' versus 'RADIATIONEXPOSURE'

P value = 0.000601 (Fisher's exact test), Q value = 0.19

Table S10. Gene #13: 'Del Peak 17(13q14.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONEXPOSURE'

nPatients	NO	YES
ALL	237	11
DEL PEAK 17(13Q14.3) MUTATED	7	4
DEL PEAK 17(13Q14.3) WILD-TYPE	230	7

Figure S10. Get High-res Image Gene #13: 'Del Peak 17(13q14.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONEXPOSURE'

'Del Peak 18(15q25.3) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.02e-14 (t-test), Q value = 1e-11

Table S11. Gene #14: 'Del Peak 18(15q25.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	225	2.8 (5.2)
DEL PEAK 18(15Q25.3) MUTATED	4	0.0 (0.0)
DEL PEAK 18(15Q25.3) WILD-TYPE	221	2.9 (5.3)

Figure S11. Get High-res Image Gene #14: 'Del Peak 18(15q25.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 26(21q21.1) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000339 (Chi-square test), Q value = 0.11

Table S12. Gene #19: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	161	32	62	25	3
DEL PEAK 26(21Q21.1) MUTATED	0	4	1	2	0
DEL PEAK 26(21Q21.1) WILD-TYPE	161	28	61	23	3

Figure S12. Get High-res Image Gene #19: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 30(Xq22.1) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000772 (Chi-square test), Q value = 0.25

Table S13. Gene #23: 'Del Peak 30(Xq22.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	161	32	62	25	3
DEL PEAK 30(XQ22.1) MUTATED	1	4	1	0	0
DEL PEAK 30(XQ22.1) WILD-TYPE	160	28	61	25	3

Figure S13. Get High-res Image Gene #23: 'Del Peak 30(Xq22.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 31(Xq22.3) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.02e-14 (t-test), Q value = 1e-11

Table S14. Gene #24: 'Del Peak 31(Xq22.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	225	2.8 (5.2)
DEL PEAK 31(XQ22.3) MUTATED	4	0.0 (0.0)
DEL PEAK 31(XQ22.3) WILD-TYPE	221	2.9 (5.3)

Figure S14. Get High-res Image Gene #24: 'Del Peak 31(Xq22.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 31(Xq22.3) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.08e-06 (Chi-square test), Q value = 0.00068

Table S15. Gene #24: 'Del Peak 31(Xq22.3) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	161	32	62	25	3
DEL PEAK 31(XQ22.3) MUTATED	0	4	0	0	0
DEL PEAK 31(XQ22.3) WILD-TYPE	161	28	62	25	3

Figure S15. Get High-res Image Gene #24: 'Del Peak 31(Xq22.3) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

Methods & Data

Input

Mutation data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = THCA-TP.clin.merged.picked.txt
Number of patients = 284
Number of significantly arm-level cnvs = 24
Number of selected clinical features = 15
Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.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

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.

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] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[3] 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)

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

[5] 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