This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 30 arm-level events and 6 molecular subtypes across 191 patients, 27 significant findings detected with P value < 0.05 and Q value < 0.25.
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8p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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11p gain cnv correlated to 'CN_CNMF'.
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11q gain cnv correlated to 'CN_CNMF'.
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21q gain cnv correlated to 'CN_CNMF'.
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22q gain cnv correlated to 'CN_CNMF'.
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5q loss cnv correlated to 'CN_CNMF'.
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7p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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7q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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15q loss cnv correlated to 'CN_CNMF'.
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16q loss cnv correlated to 'CN_CNMF'.
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17p loss cnv correlated to 'CN_CNMF'.
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17q loss cnv correlated to 'CN_CNMF'.
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18p loss cnv correlated to 'CN_CNMF'.
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18q loss cnv correlated to 'CN_CNMF'.
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xq loss cnv correlated to 'CN_CNMF'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ 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 | |
7q loss | 20 (10%) | 171 |
1e-05 (0.00174) |
4e-05 (0.00664) |
0.00618 (0.834) |
1e-05 (0.00174) |
0.00151 (0.226) |
0.00076 (0.119) |
7p loss | 17 (9%) | 174 |
4e-05 (0.00664) |
0.00012 (0.0196) |
0.00096 (0.149) |
1e-05 (0.00174) |
0.00351 (0.495) |
0.00357 (0.5) |
8p gain | 22 (12%) | 169 |
0.00084 (0.131) |
0.00049 (0.0784) |
0.0283 (1.00) |
0.00074 (0.117) |
0.0103 (1.00) |
0.0162 (1.00) |
8q gain | 23 (12%) | 168 |
0.00145 (0.219) |
0.00152 (0.226) |
0.0131 (1.00) |
0.00157 (0.232) |
0.00719 (0.942) |
0.015 (1.00) |
11p gain | 4 (2%) | 187 |
0.00071 (0.113) |
0.147 (1.00) |
0.467 (1.00) |
0.366 (1.00) |
0.527 (1.00) |
0.0226 (1.00) |
11q gain | 7 (4%) | 184 |
2e-05 (0.00338) |
0.0126 (1.00) |
0.0664 (1.00) |
0.0744 (1.00) |
0.293 (1.00) |
0.016 (1.00) |
21q gain | 8 (4%) | 183 |
1e-05 (0.00174) |
0.231 (1.00) |
0.126 (1.00) |
0.525 (1.00) |
0.0818 (1.00) |
0.411 (1.00) |
22q gain | 9 (5%) | 182 |
0.00104 (0.16) |
0.0179 (1.00) |
0.134 (1.00) |
0.0163 (1.00) |
0.055 (1.00) |
0.0127 (1.00) |
5q loss | 6 (3%) | 185 |
2e-05 (0.00338) |
0.0304 (1.00) |
0.225 (1.00) |
0.631 (1.00) |
0.0316 (1.00) |
0.0327 (1.00) |
15q loss | 4 (2%) | 187 |
0.00045 (0.0724) |
0.571 (1.00) |
0.0665 (1.00) |
0.368 (1.00) |
0.023 (1.00) |
0.184 (1.00) |
16q loss | 4 (2%) | 187 |
0.00126 (0.193) |
0.147 (1.00) |
0.785 (1.00) |
1 (1.00) |
0.0144 (1.00) |
0.0221 (1.00) |
17p loss | 13 (7%) | 178 |
1e-05 (0.00174) |
0.00449 (0.62) |
0.157 (1.00) |
0.00191 (0.279) |
0.16 (1.00) |
0.00343 (0.487) |
17q loss | 7 (4%) | 184 |
2e-05 (0.00338) |
0.214 (1.00) |
0.065 (1.00) |
0.233 (1.00) |
0.0391 (1.00) |
0.0485 (1.00) |
18p loss | 5 (3%) | 186 |
0.00033 (0.0535) |
0.0685 (1.00) |
1 (1.00) |
0.866 (1.00) |
0.247 (1.00) |
0.186 (1.00) |
18q loss | 4 (2%) | 187 |
0.00134 (0.204) |
0.145 (1.00) |
0.467 (1.00) |
0.865 (1.00) |
0.101 (1.00) |
0.184 (1.00) |
xq loss | 5 (3%) | 186 |
6e-05 (0.00984) |
0.145 (1.00) |
0.221 (1.00) |
0.631 (1.00) |
0.00331 (0.473) |
0.00462 (0.633) |
1p gain | 3 (2%) | 188 |
0.00412 (0.573) |
0.265 (1.00) |
0.187 (1.00) |
0.587 (1.00) |
0.0925 (1.00) |
0.0919 (1.00) |
4p gain | 4 (2%) | 187 |
0.0286 (1.00) |
0.0485 (1.00) |
0.341 (1.00) |
0.835 (1.00) |
||
4q gain | 4 (2%) | 187 |
0.028 (1.00) |
0.0495 (1.00) |
0.345 (1.00) |
0.834 (1.00) |
||
10q gain | 3 (2%) | 188 |
0.0148 (1.00) |
0.266 (1.00) |
0.185 (1.00) |
0.589 (1.00) |
0.554 (1.00) |
0.0913 (1.00) |
13q gain | 6 (3%) | 185 |
0.0418 (1.00) |
0.0293 (1.00) |
0.124 (1.00) |
0.0832 (1.00) |
0.802 (1.00) |
0.074 (1.00) |
17q gain | 3 (2%) | 188 |
0.00621 (0.834) |
0.302 (1.00) |
1 (1.00) |
0.59 (1.00) |
0.482 (1.00) |
0.307 (1.00) |
19p gain | 5 (3%) | 186 |
0.0127 (1.00) |
0.643 (1.00) |
1 (1.00) |
0.864 (1.00) |
0.578 (1.00) |
1 (1.00) |
19q gain | 5 (3%) | 186 |
0.0127 (1.00) |
0.645 (1.00) |
1 (1.00) |
0.865 (1.00) |
0.581 (1.00) |
1 (1.00) |
xq gain | 3 (2%) | 188 |
0.00174 (0.256) |
0.882 (1.00) |
0.891 (1.00) |
0.0452 (1.00) |
||
3p loss | 3 (2%) | 188 |
0.00707 (0.933) |
0.264 (1.00) |
0.787 (1.00) |
1 (1.00) |
0.0615 (1.00) |
0.0918 (1.00) |
3q loss | 3 (2%) | 188 |
0.0067 (0.891) |
0.266 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.0617 (1.00) |
0.0938 (1.00) |
12p loss | 4 (2%) | 187 |
0.00599 (0.815) |
0.0952 (1.00) |
0.375 (1.00) |
0.39 (1.00) |
0.484 (1.00) |
0.185 (1.00) |
19p loss | 4 (2%) | 187 |
0.00307 (0.442) |
0.536 (1.00) |
0.465 (1.00) |
0.865 (1.00) |
0.312 (1.00) |
0.248 (1.00) |
19q loss | 4 (2%) | 187 |
0.00298 (0.432) |
0.536 (1.00) |
0.468 (1.00) |
0.864 (1.00) |
0.314 (1.00) |
0.251 (1.00) |
P value = 0.00084 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
8P GAIN MUTATED | 11 | 1 | 10 | 0 |
8P GAIN WILD-TYPE | 137 | 13 | 17 | 2 |
P value = 0.00049 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
8P GAIN MUTATED | 2 | 1 | 16 | 0 | 2 |
8P GAIN WILD-TYPE | 44 | 43 | 45 | 14 | 18 |
P value = 0.00074 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
8P GAIN MUTATED | 1 | 0 | 0 | 15 | 1 | 1 |
8P GAIN WILD-TYPE | 15 | 13 | 14 | 40 | 25 | 41 |
P value = 0.00145 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
8Q GAIN MUTATED | 12 | 1 | 10 | 0 |
8Q GAIN WILD-TYPE | 136 | 13 | 17 | 2 |
P value = 0.00152 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
8Q GAIN MUTATED | 2 | 2 | 16 | 0 | 2 |
8Q GAIN WILD-TYPE | 44 | 42 | 45 | 14 | 18 |
P value = 0.00157 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
8Q GAIN MUTATED | 1 | 0 | 1 | 15 | 1 | 1 |
8Q GAIN WILD-TYPE | 15 | 13 | 13 | 40 | 25 | 41 |
P value = 0.00071 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
11P GAIN MUTATED | 0 | 3 | 1 | 0 |
11P GAIN WILD-TYPE | 148 | 11 | 26 | 2 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
11Q GAIN MUTATED | 0 | 4 | 3 | 0 |
11Q GAIN WILD-TYPE | 148 | 10 | 24 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
21Q GAIN MUTATED | 0 | 0 | 8 | 0 |
21Q GAIN WILD-TYPE | 148 | 14 | 19 | 2 |
P value = 0.00104 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
22Q GAIN MUTATED | 2 | 2 | 5 | 0 |
22Q GAIN WILD-TYPE | 146 | 12 | 22 | 2 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
5Q LOSS MUTATED | 0 | 0 | 6 | 0 |
5Q LOSS WILD-TYPE | 148 | 14 | 21 | 2 |
P value = 4e-05 (Fisher's exact test), Q value = 0.0066
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
7P LOSS MUTATED | 7 | 0 | 9 | 1 |
7P LOSS WILD-TYPE | 141 | 14 | 18 | 1 |
P value = 0.00012 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
7P LOSS MUTATED | 1 | 0 | 14 | 1 | 1 |
7P LOSS WILD-TYPE | 45 | 44 | 47 | 13 | 19 |
P value = 0.00096 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 52 | 44 |
7P LOSS MUTATED | 13 | 0 | 3 |
7P LOSS WILD-TYPE | 57 | 52 | 41 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
7P LOSS MUTATED | 0 | 0 | 0 | 16 | 0 | 0 |
7P LOSS WILD-TYPE | 16 | 13 | 14 | 39 | 26 | 42 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
7Q LOSS MUTATED | 8 | 0 | 11 | 1 |
7Q LOSS WILD-TYPE | 140 | 14 | 16 | 1 |
P value = 4e-05 (Fisher's exact test), Q value = 0.0066
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
7Q LOSS MUTATED | 1 | 0 | 17 | 1 | 1 |
7Q LOSS WILD-TYPE | 45 | 44 | 44 | 13 | 19 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 16 | 13 | 14 | 55 | 26 | 42 |
7Q LOSS MUTATED | 0 | 0 | 0 | 17 | 0 | 0 |
7Q LOSS WILD-TYPE | 16 | 13 | 14 | 38 | 26 | 42 |
P value = 0.00151 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 37 | 41 | 43 |
7Q LOSS MUTATED | 1 | 10 | 4 | 4 |
7Q LOSS WILD-TYPE | 57 | 27 | 37 | 39 |
P value = 0.00076 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
7Q LOSS MUTATED | 1 | 8 | 10 |
7Q LOSS WILD-TYPE | 66 | 26 | 68 |
P value = 0.00045 (Fisher's exact test), Q value = 0.072
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
15Q LOSS MUTATED | 0 | 0 | 3 | 1 |
15Q LOSS WILD-TYPE | 148 | 14 | 24 | 1 |
P value = 0.00126 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
16Q LOSS MUTATED | 0 | 0 | 4 | 0 |
16Q LOSS WILD-TYPE | 148 | 14 | 23 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
17P LOSS MUTATED | 0 | 0 | 13 | 0 |
17P LOSS WILD-TYPE | 148 | 14 | 14 | 2 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
17Q LOSS MUTATED | 0 | 0 | 7 | 0 |
17Q LOSS WILD-TYPE | 148 | 14 | 20 | 2 |
P value = 0.00033 (Fisher's exact test), Q value = 0.053
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
18P LOSS MUTATED | 0 | 0 | 5 | 0 |
18P LOSS WILD-TYPE | 148 | 14 | 22 | 2 |
P value = 0.00134 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
18Q LOSS MUTATED | 0 | 0 | 4 | 0 |
18Q LOSS WILD-TYPE | 148 | 14 | 23 | 2 |
P value = 6e-05 (Fisher's exact test), Q value = 0.0098
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 14 | 27 | 2 |
XQ LOSS MUTATED | 0 | 0 | 4 | 1 |
XQ LOSS WILD-TYPE | 148 | 14 | 23 | 1 |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtypes file = LAML-TB.transferedmergedcluster.txt
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Number of patients = 191
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Number of significantly arm-level cnvs = 30
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Number of molecular subtypes = 6
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Exclude genes that fewer than K tumors have mutations, 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.