Correlation between copy number variation genes (focal events) and selected clinical features
Thymoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1416WK9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1416WK9
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 18 focal events and 8 clinical features across 123 patients, 24 significant findings detected with Q value < 0.25.

  • amp_1q41 cnv correlated to 'Time to Death',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_12p12.3 cnv correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.

  • amp_17q11.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_21q22.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_xq23 cnv correlated to 'Time to Death'.

  • del_2q37.1 cnv correlated to 'ETHNICITY'.

  • del_3p22.2 cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.

  • del_6p25.2 cnv correlated to 'Time to Death',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_6q21 cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.

  • del_9p22.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_9p21.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_19p13.11 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_22q12.1 cnv correlated to 'YEARS_TO_BIRTH' and 'ETHNICITY'.

  • del_22q13.32 cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 18 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 24 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		TUMOR
TISSUE
SITE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-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
amp 1q41 28 (23%) 95 0.0012
(0.0172) 		0.0831
(0.323) 		1
(1.00) 		0.138
(0.413) 		0.000234
(0.0042) 		1e-05
(0.00048) 		1
(1.00) 		0.443
(0.787)
del 6p25 2 26 (21%) 97 0.00453
(0.05) 		0.718
(0.984) 		1
(1.00) 		1
(1.00) 		0.645
(0.941) 		0.00323
(0.0423) 		0.274
(0.616) 		0.0236
(0.148)
del 22q13 32 15 (12%) 108 0.763
(1.00) 		0.0284
(0.17) 		0.0947
(0.359) 		0.411
(0.769) 		0.144
(0.423) 		0.00907
(0.0768) 		1
(1.00) 		0.0199
(0.136)
amp 12p12 3 6 (5%) 117 0.297
(0.649) 		0.102
(0.368) 		0.0207
(0.136) 		1
(1.00) 		1
(1.00) 		0.00071
(0.0114) 		1
(1.00) 		0.0767
(0.307)
del 3p22 2 14 (11%) 109 0.199
(0.522) 		0.656
(0.941) 		0.187
(0.515) 		1
(1.00) 		0.552
(0.903) 		0.0119
(0.0856) 		1
(1.00) 		0.0113
(0.0856)
del 6q21 20 (16%) 103 0.0594
(0.296) 		0.187
(0.515) 		0.379
(0.758) 		0.626
(0.939) 		0.609
(0.939) 		9e-05
(0.00259) 		0.501
(0.839) 		0.00593
(0.0569)
del 22q12 1 19 (15%) 104 0.369
(0.749) 		0.0102
(0.0819) 		0.128
(0.401) 		0.455
(0.792) 		0.797
(1.00) 		0.0675
(0.296) 		0.871
(1.00) 		0.00777
(0.0699)
amp 17q11 2 10 (8%) 113 0.396
(0.769) 		0.207
(0.533) 		0.456
(0.792) 		1
(1.00) 		0.307
(0.65) 		0.00012
(0.00288) 		1
(1.00) 		0.192
(0.515)
amp 21q22 2 3 (2%) 120 0.782
(1.00) 		0.221
(0.551) 		0.121
(0.39) 		0.107
(0.368) 		1
(1.00) 		0.00486
(0.05) 		1
(1.00) 		1
(1.00)
amp xq23 7 (6%) 116 8.63e-06
(0.00048) 		0.0582
(0.296) 		0.648
(0.941) 		1
(1.00) 		0.229
(0.551) 		0.103
(0.368) 		1
(1.00) 		1
(1.00)
del 2q37 1 5 (4%) 118 0.62
(0.939) 		0.333
(0.694) 		0.0699
(0.296) 		1
(1.00) 		0.66
(0.941) 		0.431
(0.775) 		0.303
(0.65) 		0.00367
(0.044)
del 9p22 1 6 (5%) 117 0.609
(0.939) 		0.0613
(0.296) 		0.119
(0.39) 		0.425
(0.775) 		0.41
(0.769) 		0.00014
(0.00288) 		1
(1.00) 		0.0767
(0.307)
del 9p21 3 11 (9%) 112 0.476
(0.816) 		0.122
(0.39) 		0.705
(0.982) 		0.35
(0.72) 		1
(1.00) 		1e-05
(0.00048) 		1
(1.00) 		0.225
(0.551)
del 19p13 11 5 (4%) 118 0.668
(0.943) 		0.0628
(0.296) 		0.0699
(0.296) 		0.193
(0.515) 		1
(1.00) 		5e-05
(0.0018) 		1
(1.00) 		0.0535
(0.296)
amp 10q11 21 3 (2%) 120 0.709
(0.982) 		0.487
(0.826) 		1
(1.00) 		0.107
(0.368) 		0.268
(0.613) 		0.138
(0.413) 		0.401
(0.769) 		1
(1.00)
amp xp11 22 3 (2%) 120 0.618
(0.939) 		0.791
(1.00) 		1
(1.00) 		0.607
(0.939) 		0.268
(0.613) 		0.0664
(0.296) 		1
(1.00) 		1
(1.00)
del 7q36 3 3 (2%) 120 0.779
(1.00) 		0.62
(0.939) 		0.528
(0.874) 		0.607
(0.939) 		0.268
(0.613) 		0.0452
(0.261) 		1
(1.00) 		0.23
(0.551)
del 10q26 3 6 (5%) 117 0.168
(0.485) 		0.845
(1.00) 		1
(1.00) 		0.425
(0.775) 		1
(1.00) 		0.297
(0.649) 		0.651
(0.941) 		0.411
(0.769)
'amp_1q41' versus 'Time to Death'

P value = 0.0012 (logrank test), Q value = 0.017

Table S1.  Gene #1: 'amp_1q41' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.4 (40.6)
AMP PEAK 1(1Q41) MUTATED 28 6 1.6 - 123.7 (40.6)
AMP PEAK 1(1Q41) WILD-TYPE 94 3 0.5 - 150.4 (40.6)

Figure S1.  Get High-res Image Gene #1: 'amp_1q41' versus Clinical Feature #1: 'Time to Death'

'amp_1q41' versus 'RADIATION_THERAPY'

P value = 0.000234 (Fisher's exact test), Q value = 0.0042

Table S2.  Gene #1: 'amp_1q41' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 81 42
AMP PEAK 1(1Q41) MUTATED 10 18
AMP PEAK 1(1Q41) WILD-TYPE 71 24

Figure S2.  Get High-res Image Gene #1: 'amp_1q41' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_1q41' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S3.  Gene #1: 'amp_1q41' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
AMP PEAK 1(1Q41) MUTATED 1 2 2 8 7 8
AMP PEAK 1(1Q41) WILD-TYPE 16 36 13 22 5 3

Figure S3.  Get High-res Image Gene #1: 'amp_1q41' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_12p12.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.0207 (Fisher's exact test), Q value = 0.14

Table S4.  Gene #3: 'amp_12p12.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients ANTERIOR MEDIASTINUM THYMUS
ALL 27 96
AMP PEAK 3(12P12.3) MUTATED 4 2
AMP PEAK 3(12P12.3) WILD-TYPE 23 94

Figure S4.  Get High-res Image Gene #3: 'amp_12p12.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_12p12.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00071 (Fisher's exact test), Q value = 0.011

Table S5.  Gene #3: 'amp_12p12.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
AMP PEAK 3(12P12.3) MUTATED 1 0 0 1 0 4
AMP PEAK 3(12P12.3) WILD-TYPE 16 38 15 29 12 7

Figure S5.  Get High-res Image Gene #3: 'amp_12p12.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_17q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0029

Table S6.  Gene #4: 'amp_17q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
AMP PEAK 4(17Q11.2) MUTATED 2 0 0 1 2 5
AMP PEAK 4(17Q11.2) WILD-TYPE 15 38 15 29 10 6

Figure S6.  Get High-res Image Gene #4: 'amp_17q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_21q22.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00486 (Fisher's exact test), Q value = 0.05

Table S7.  Gene #5: 'amp_21q22.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
AMP PEAK 5(21Q22.2) MUTATED 0 0 0 0 1 2
AMP PEAK 5(21Q22.2) WILD-TYPE 17 38 15 30 11 9

Figure S7.  Get High-res Image Gene #5: 'amp_21q22.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_xq23' versus 'Time to Death'

P value = 8.63e-06 (logrank test), Q value = 0.00048

Table S8.  Gene #7: 'amp_xq23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.4 (40.6)
AMP PEAK 7(XQ23) MUTATED 7 3 1.6 - 81.8 (25.6)
AMP PEAK 7(XQ23) WILD-TYPE 115 6 0.5 - 150.4 (41.2)

Figure S8.  Get High-res Image Gene #7: 'amp_xq23' versus Clinical Feature #1: 'Time to Death'

'del_2q37.1' versus 'ETHNICITY'

P value = 0.00367 (Fisher's exact test), Q value = 0.044

Table S9.  Gene #8: 'del_2q37.1' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
DEL PEAK 1(2Q37.1) MUTATED 3 2
DEL PEAK 1(2Q37.1) WILD-TYPE 6 98

Figure S9.  Get High-res Image Gene #8: 'del_2q37.1' versus Clinical Feature #8: 'ETHNICITY'

'del_3p22.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0119 (Fisher's exact test), Q value = 0.086

Table S10.  Gene #9: 'del_3p22.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
DEL PEAK 2(3P22.2) MUTATED 0 2 0 6 4 2
DEL PEAK 2(3P22.2) WILD-TYPE 17 36 15 24 8 9

Figure S10.  Get High-res Image Gene #9: 'del_3p22.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_3p22.2' versus 'ETHNICITY'

P value = 0.0113 (Fisher's exact test), Q value = 0.086

Table S11.  Gene #9: 'del_3p22.2' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
DEL PEAK 2(3P22.2) MUTATED 4 9
DEL PEAK 2(3P22.2) WILD-TYPE 5 91

Figure S11.  Get High-res Image Gene #9: 'del_3p22.2' versus Clinical Feature #8: 'ETHNICITY'

'del_6p25.2' versus 'Time to Death'

P value = 0.00453 (logrank test), Q value = 0.05

Table S12.  Gene #10: 'del_6p25.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.4 (40.6)
DEL PEAK 3(6P25.2) MUTATED 25 5 4.1 - 120.4 (31.9)
DEL PEAK 3(6P25.2) WILD-TYPE 97 4 0.5 - 150.4 (42.1)

Figure S12.  Get High-res Image Gene #10: 'del_6p25.2' versus Clinical Feature #1: 'Time to Death'

'del_6p25.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00323 (Fisher's exact test), Q value = 0.042

Table S13.  Gene #10: 'del_6p25.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
DEL PEAK 3(6P25.2) MUTATED 2 5 0 8 5 6
DEL PEAK 3(6P25.2) WILD-TYPE 15 33 15 22 7 5

Figure S13.  Get High-res Image Gene #10: 'del_6p25.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_6p25.2' versus 'ETHNICITY'

P value = 0.0236 (Fisher's exact test), Q value = 0.15

Table S14.  Gene #10: 'del_6p25.2' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
DEL PEAK 3(6P25.2) MUTATED 5 19
DEL PEAK 3(6P25.2) WILD-TYPE 4 81

Figure S14.  Get High-res Image Gene #10: 'del_6p25.2' versus Clinical Feature #8: 'ETHNICITY'

'del_6q21' versus 'HISTOLOGICAL_TYPE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0026

Table S15.  Gene #11: 'del_6q21' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
DEL PEAK 4(6Q21) MUTATED 0 2 0 8 5 5
DEL PEAK 4(6Q21) WILD-TYPE 17 36 15 22 7 6

Figure S15.  Get High-res Image Gene #11: 'del_6q21' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_6q21' versus 'ETHNICITY'

P value = 0.00593 (Fisher's exact test), Q value = 0.057

Table S16.  Gene #11: 'del_6q21' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
DEL PEAK 4(6Q21) MUTATED 5 13
DEL PEAK 4(6Q21) WILD-TYPE 4 87

Figure S16.  Get High-res Image Gene #11: 'del_6q21' versus Clinical Feature #8: 'ETHNICITY'

'del_9p22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00014 (Fisher's exact test), Q value = 0.0029

Table S17.  Gene #13: 'del_9p22.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
DEL PEAK 6(9P22.1) MUTATED 1 0 0 0 1 4
DEL PEAK 6(9P22.1) WILD-TYPE 16 38 15 30 11 7

Figure S17.  Get High-res Image Gene #13: 'del_9p22.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S18.  Gene #14: 'del_9p21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
DEL PEAK 7(9P21.3) MUTATED 1 1 0 0 2 7
DEL PEAK 7(9P21.3) WILD-TYPE 16 37 15 30 10 4

Figure S18.  Get High-res Image Gene #14: 'del_9p21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_19p13.11' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0018

Table S19.  Gene #16: 'del_19p13.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
DEL PEAK 9(19P13.11) MUTATED 0 0 0 0 1 4
DEL PEAK 9(19P13.11) WILD-TYPE 17 38 15 30 11 7

Figure S19.  Get High-res Image Gene #16: 'del_19p13.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_22q12.1' versus 'YEARS_TO_BIRTH'

P value = 0.0102 (Wilcoxon-test), Q value = 0.082

Table S20.  Gene #17: 'del_22q12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 122 58.3 (13.0)
DEL PEAK 10(22Q12.1) MUTATED 18 65.3 (11.3)
DEL PEAK 10(22Q12.1) WILD-TYPE 104 57.0 (12.9)

Figure S20.  Get High-res Image Gene #17: 'del_22q12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q12.1' versus 'ETHNICITY'

P value = 0.00777 (Fisher's exact test), Q value = 0.07

Table S21.  Gene #17: 'del_22q12.1' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
DEL PEAK 10(22Q12.1) MUTATED 5 14
DEL PEAK 10(22Q12.1) WILD-TYPE 4 86

Figure S21.  Get High-res Image Gene #17: 'del_22q12.1' versus Clinical Feature #8: 'ETHNICITY'

'del_22q13.32' versus 'YEARS_TO_BIRTH'

P value = 0.0284 (Wilcoxon-test), Q value = 0.17

Table S22.  Gene #18: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 122 58.3 (13.0)
DEL PEAK 11(22Q13.32) MUTATED 15 64.7 (11.2)
DEL PEAK 11(22Q13.32) WILD-TYPE 107 57.4 (13.0)

Figure S22.  Get High-res Image Gene #18: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 0.00907 (Fisher's exact test), Q value = 0.077

Table S23.  Gene #18: 'del_22q13.32' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
DEL PEAK 11(22Q13.32) MUTATED 2 3 0 2 3 5
DEL PEAK 11(22Q13.32) WILD-TYPE 15 35 15 28 9 6

Figure S23.  Get High-res Image Gene #18: 'del_22q13.32' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'ETHNICITY'

P value = 0.0199 (Fisher's exact test), Q value = 0.14

Table S24.  Gene #18: 'del_22q13.32' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
DEL PEAK 11(22Q13.32) MUTATED 4 11
DEL PEAK 11(22Q13.32) WILD-TYPE 5 89

Figure S24.  Get High-res Image Gene #18: 'del_22q13.32' versus Clinical Feature #8: 'ETHNICITY'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/22516313/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THYM-TP/22507339/THYM-TP.merged_data.txt

  • Number of patients = 123

  • Number of significantly focal cnvs = 18

  • Number of selected clinical features = 8

  • 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

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