This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 20 focal events and 10 molecular subtypes across 36 patients, 18 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_11q13.3 cnv correlated to 'RPPA_CHIERARCHICAL'.
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del_1p36.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_3p13 cnv correlated to 'CN_CNMF'.
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del_6q13 cnv correlated to 'CN_CNMF'.
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del_9q21.11 cnv correlated to 'RPPA_CHIERARCHICAL'.
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del_12q24.13 cnv correlated to 'CN_CNMF'.
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del_13q21.32 cnv correlated to 'CN_CNMF'.
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del_14q22.1 cnv correlated to 'RPPA_CHIERARCHICAL'.
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del_14q32.11 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_14q32.13 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_14q32.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_16q23.1 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
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 | Fisher's exact test | Fisher's exact test | |
del 1p36 21 | 30 (83%) | 6 |
0.0168 (0.213) |
0.00218 (0.0872) |
0.106 (0.583) |
0.291 (0.719) |
0.00018 (0.0167) |
0.00883 (0.206) |
0.55 (0.797) |
0.128 (0.596) |
0.473 (0.763) |
0.255 (0.699) |
del 14q32 11 | 20 (56%) | 16 |
0.00034 (0.017) |
0.00943 (0.206) |
0.267 (0.699) |
0.472 (0.763) |
0.0407 (0.37) |
0.0576 (0.421) |
0.908 (0.977) |
0.755 (0.916) |
0.355 (0.728) |
0.532 (0.777) |
del 14q32 13 | 20 (56%) | 16 |
0.00025 (0.0167) |
0.0103 (0.206) |
0.265 (0.699) |
0.471 (0.763) |
0.0405 (0.37) |
0.0575 (0.421) |
0.908 (0.977) |
0.755 (0.916) |
0.356 (0.728) |
0.531 (0.777) |
del 14q32 33 | 20 (56%) | 16 |
0.00021 (0.0167) |
0.0102 (0.206) |
0.267 (0.699) |
0.473 (0.763) |
0.0395 (0.37) |
0.0572 (0.421) |
0.909 (0.977) |
0.756 (0.916) |
0.354 (0.728) |
0.532 (0.777) |
amp 11q13 3 | 8 (22%) | 28 |
0.411 (0.744) |
0.609 (0.84) |
0.152 (0.646) |
0.019 (0.213) |
0.518 (0.777) |
0.0448 (0.389) |
0.388 (0.728) |
0.971 (1.00) |
0.246 (0.699) |
0.719 (0.913) |
del 3p13 | 28 (78%) | 8 |
0.0163 (0.213) |
0.364 (0.728) |
0.621 (0.84) |
0.373 (0.728) |
0.38 (0.728) |
0.289 (0.719) |
0.812 (0.935) |
0.241 (0.699) |
0.563 (0.81) |
0.371 (0.728) |
del 6q13 | 21 (58%) | 15 |
0.0147 (0.213) |
0.119 (0.583) |
0.454 (0.763) |
0.179 (0.646) |
0.157 (0.646) |
0.252 (0.699) |
0.878 (0.975) |
0.344 (0.728) |
0.961 (1.00) |
0.916 (0.977) |
del 9q21 11 | 19 (53%) | 17 |
0.0293 (0.309) |
0.492 (0.768) |
0.256 (0.699) |
0.0115 (0.209) |
0.162 (0.646) |
0.187 (0.649) |
0.251 (0.699) |
0.43 (0.754) |
0.298 (0.72) |
0.347 (0.728) |
del 12q24 13 | 8 (22%) | 28 |
0.0192 (0.213) |
0.782 (0.935) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.615 (0.84) |
0.811 (0.935) |
0.669 (0.886) |
0.721 (0.913) |
0.812 (0.935) |
del 13q21 32 | 16 (44%) | 20 |
0.0175 (0.213) |
0.918 (0.977) |
0.526 (0.777) |
0.478 (0.764) |
0.0979 (0.576) |
0.875 (0.975) |
0.588 (0.834) |
0.488 (0.768) |
0.882 (0.975) |
0.513 (0.777) |
del 14q22 1 | 14 (39%) | 22 |
0.0869 (0.561) |
0.575 (0.821) |
0.25 (0.699) |
0.00744 (0.206) |
0.383 (0.728) |
0.12 (0.583) |
0.88 (0.975) |
0.973 (1.00) |
0.832 (0.951) |
0.38 (0.728) |
del 16q23 1 | 7 (19%) | 29 |
0.181 (0.646) |
0.274 (0.699) |
0.39 (0.728) |
0.429 (0.754) |
0.19 (0.649) |
0.413 (0.744) |
0.595 (0.838) |
0.019 (0.213) |
0.619 (0.84) |
0.702 (0.906) |
amp 1q22 | 24 (67%) | 12 |
0.321 (0.728) |
0.367 (0.728) |
0.703 (0.906) |
0.74 (0.916) |
0.0589 (0.421) |
0.355 (0.728) |
1 (1.00) |
0.403 (0.74) |
0.163 (0.646) |
0.392 (0.728) |
amp 12q13 2 | 10 (28%) | 26 |
0.271 (0.699) |
0.897 (0.977) |
0.0638 (0.44) |
0.192 (0.649) |
0.742 (0.916) |
0.91 (0.977) |
0.426 (0.754) |
0.518 (0.777) |
0.948 (1.00) |
0.47 (0.763) |
del 3p25 3 | 28 (78%) | 8 |
0.109 (0.583) |
0.609 (0.84) |
1 (1.00) |
0.388 (0.728) |
0.122 (0.583) |
0.0702 (0.468) |
0.503 (0.777) |
0.761 (0.916) |
0.721 (0.913) |
0.221 (0.699) |
del 4q34 3 | 23 (64%) | 13 |
0.255 (0.699) |
0.467 (0.763) |
0.111 (0.583) |
0.168 (0.646) |
0.347 (0.728) |
0.332 (0.728) |
0.264 (0.699) |
0.486 (0.768) |
0.507 (0.777) |
0.168 (0.646) |
del 5q13 3 | 8 (22%) | 28 |
0.242 (0.699) |
0.276 (0.699) |
0.393 (0.728) |
0.3 (0.72) |
0.0497 (0.415) |
0.159 (0.646) |
1 (1.00) |
0.669 (0.886) |
0.735 (0.916) |
0.879 (0.975) |
del 9p21 3 | 23 (64%) | 13 |
0.254 (0.699) |
0.472 (0.763) |
0.809 (0.935) |
0.159 (0.646) |
0.364 (0.728) |
0.16 (0.646) |
0.108 (0.583) |
0.621 (0.84) |
0.813 (0.935) |
0.122 (0.583) |
del 10q26 12 | 12 (33%) | 24 |
0.861 (0.975) |
0.175 (0.646) |
1 (1.00) |
0.808 (0.935) |
0.698 (0.906) |
0.684 (0.9) |
0.456 (0.763) |
0.215 (0.699) |
0.464 (0.763) |
0.309 (0.728) |
del 11q25 | 13 (36%) | 23 |
0.096 (0.576) |
1 (1.00) |
0.302 (0.72) |
0.0913 (0.571) |
0.364 (0.728) |
0.638 (0.857) |
0.796 (0.935) |
0.217 (0.699) |
0.726 (0.913) |
0.172 (0.646) |
P value = 0.019 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 6 | 7 | 8 | 9 |
AMP PEAK 2(11Q13.3) MUTATED | 2 | 0 | 4 | 0 |
AMP PEAK 2(11Q13.3) WILD-TYPE | 4 | 7 | 4 | 9 |
P value = 0.0168 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 9 | 7 | 6 |
DEL PEAK 1(1P36.21) MUTATED | 8 | 9 | 7 | 6 |
DEL PEAK 1(1P36.21) WILD-TYPE | 6 | 0 | 0 | 0 |
P value = 0.00218 (Fisher's exact test), Q value = 0.087
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 10 | 12 |
DEL PEAK 1(1P36.21) MUTATED | 8 | 10 | 12 |
DEL PEAK 1(1P36.21) WILD-TYPE | 6 | 0 | 0 |
P value = 0.00018 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 6 | 4 | 5 | 6 | 9 | 6 |
DEL PEAK 1(1P36.21) MUTATED | 1 | 4 | 4 | 6 | 9 | 6 |
DEL PEAK 1(1P36.21) WILD-TYPE | 5 | 0 | 1 | 0 | 0 | 0 |
P value = 0.00883 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 4 | 5 | 5 | 9 | 6 | 5 | 2 |
DEL PEAK 1(1P36.21) MUTATED | 1 | 4 | 4 | 9 | 6 | 5 | 1 |
DEL PEAK 1(1P36.21) WILD-TYPE | 3 | 1 | 1 | 0 | 0 | 0 | 1 |
P value = 0.0163 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 9 | 7 | 6 |
DEL PEAK 3(3P13) MUTATED | 7 | 8 | 7 | 6 |
DEL PEAK 3(3P13) WILD-TYPE | 7 | 1 | 0 | 0 |
P value = 0.0147 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 9 | 7 | 6 |
DEL PEAK 6(6Q13) MUTATED | 6 | 3 | 7 | 5 |
DEL PEAK 6(6Q13) WILD-TYPE | 8 | 6 | 0 | 1 |
P value = 0.0115 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 6 | 7 | 8 | 9 |
DEL PEAK 8(9Q21.11) MUTATED | 4 | 3 | 7 | 1 |
DEL PEAK 8(9Q21.11) WILD-TYPE | 2 | 4 | 1 | 8 |
P value = 0.0192 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 9 | 7 | 6 |
DEL PEAK 11(12Q24.13) MUTATED | 1 | 4 | 0 | 3 |
DEL PEAK 11(12Q24.13) WILD-TYPE | 13 | 5 | 7 | 3 |
P value = 0.0175 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 9 | 7 | 6 |
DEL PEAK 12(13Q21.32) MUTATED | 5 | 1 | 5 | 5 |
DEL PEAK 12(13Q21.32) WILD-TYPE | 9 | 8 | 2 | 1 |
P value = 0.00744 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 6 | 7 | 8 | 9 |
DEL PEAK 13(14Q22.1) MUTATED | 0 | 2 | 6 | 1 |
DEL PEAK 13(14Q22.1) WILD-TYPE | 6 | 5 | 2 | 8 |
P value = 0.00034 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 9 | 7 | 6 |
DEL PEAK 14(14Q32.11) MUTATED | 2 | 6 | 6 | 6 |
DEL PEAK 14(14Q32.11) WILD-TYPE | 12 | 3 | 1 | 0 |
P value = 0.00943 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 10 | 12 |
DEL PEAK 14(14Q32.11) MUTATED | 4 | 9 | 7 |
DEL PEAK 14(14Q32.11) WILD-TYPE | 10 | 1 | 5 |
P value = 0.00025 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 9 | 7 | 6 |
DEL PEAK 15(14Q32.13) MUTATED | 2 | 6 | 6 | 6 |
DEL PEAK 15(14Q32.13) WILD-TYPE | 12 | 3 | 1 | 0 |
P value = 0.0103 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 10 | 12 |
DEL PEAK 15(14Q32.13) MUTATED | 4 | 9 | 7 |
DEL PEAK 15(14Q32.13) WILD-TYPE | 10 | 1 | 5 |
P value = 0.00021 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 14 | 9 | 7 | 6 |
DEL PEAK 16(14Q32.33) MUTATED | 2 | 6 | 6 | 6 |
DEL PEAK 16(14Q32.33) WILD-TYPE | 12 | 3 | 1 | 0 |
P value = 0.0102 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 10 | 12 |
DEL PEAK 16(14Q32.33) MUTATED | 4 | 9 | 7 |
DEL PEAK 16(14Q32.33) WILD-TYPE | 10 | 1 | 5 |
P value = 0.019 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 8 | 10 | 4 | 5 | 5 | 4 |
DEL PEAK 17(16Q23.1) MUTATED | 1 | 2 | 0 | 0 | 4 | 0 |
DEL PEAK 17(16Q23.1) WILD-TYPE | 7 | 8 | 4 | 5 | 1 | 4 |
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Copy number data file = all_lesions.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/22519029/transformed.cor.cli.txt
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Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/22541054/CHOL-TP.transferedmergedcluster.txt
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Number of patients = 36
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Number of significantly focal cnvs = 20
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Number of molecular subtypes = 10
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Exclude genes that fewer than K tumors have alterations, K = 3
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
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.
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.