This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 23 focal events and 8 molecular subtypes across 37 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.
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del_3p21.1 cnv correlated to 'MIRSEQ_CNMF'.
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del_9p21.3 cnv correlated to 'CN_CNMF'.
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 | |
del 3p21 1 | 21 (57%) | 16 |
0.519 (1.00) |
0.746 (1.00) |
0.315 (1.00) |
0.00807 (1.00) |
0.000723 (0.129) |
0.0582 (1.00) |
0.00172 (0.305) |
0.00618 (1.00) |
del 9p21 3 | 23 (62%) | 14 |
2.1e-05 (0.00378) |
1 (1.00) |
0.164 (1.00) |
0.0675 (1.00) |
1 (1.00) |
0.297 (1.00) |
1 (1.00) |
0.458 (1.00) |
amp 12p11 21 | 10 (27%) | 27 |
0.00948 (1.00) |
0.46 (1.00) |
0.711 (1.00) |
0.517 (1.00) |
1 (1.00) |
0.574 (1.00) |
0.665 (1.00) |
0.914 (1.00) |
amp 17q24 3 | 12 (32%) | 25 |
0.0768 (1.00) |
1 (1.00) |
0.725 (1.00) |
0.373 (1.00) |
1 (1.00) |
0.0665 (1.00) |
0.665 (1.00) |
0.418 (1.00) |
amp 19q13 43 | 4 (11%) | 33 |
0.296 (1.00) |
1 (1.00) |
0.603 (1.00) |
0.178 (1.00) |
1 (1.00) |
0.597 (1.00) |
1 (1.00) |
0.412 (1.00) |
amp 20p12 1 | 4 (11%) | 33 |
0.618 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
del 1p36 23 | 17 (46%) | 20 |
0.00298 (0.521) |
1 (1.00) |
1 (1.00) |
0.209 (1.00) |
0.688 (1.00) |
0.0651 (1.00) |
0.695 (1.00) |
0.0203 (1.00) |
del 1p22 1 | 17 (46%) | 20 |
0.104 (1.00) |
0.0994 (1.00) |
0.738 (1.00) |
0.916 (1.00) |
1 (1.00) |
0.541 (1.00) |
1 (1.00) |
0.612 (1.00) |
del 2q35 | 8 (22%) | 29 |
0.0554 (1.00) |
0.428 (1.00) |
1 (1.00) |
0.879 (1.00) |
1 (1.00) |
0.213 (1.00) |
0.598 (1.00) |
0.163 (1.00) |
del 4q26 | 18 (49%) | 19 |
0.00814 (1.00) |
0.103 (1.00) |
0.0184 (1.00) |
0.0471 (1.00) |
1 (1.00) |
0.136 (1.00) |
1 (1.00) |
0.112 (1.00) |
del 5q23 2 | 7 (19%) | 30 |
0.202 (1.00) |
0.416 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.913 (1.00) |
1 (1.00) |
0.541 (1.00) |
del 6q22 31 | 20 (54%) | 17 |
0.508 (1.00) |
0.517 (1.00) |
0.315 (1.00) |
0.0996 (1.00) |
1 (1.00) |
0.0983 (1.00) |
1 (1.00) |
0.216 (1.00) |
del 10p15 1 | 13 (35%) | 24 |
0.0357 (1.00) |
0.512 (1.00) |
0.164 (1.00) |
0.172 (1.00) |
1 (1.00) |
0.393 (1.00) |
0.692 (1.00) |
0.254 (1.00) |
del 10q22 3 | 7 (19%) | 30 |
0.437 (1.00) |
0.68 (1.00) |
0.402 (1.00) |
0.335 (1.00) |
1 (1.00) |
0.756 (1.00) |
0.365 (1.00) |
0.14 (1.00) |
del 10q24 1 | 13 (35%) | 24 |
0.489 (1.00) |
0.731 (1.00) |
1 (1.00) |
0.561 (1.00) |
0.228 (1.00) |
0.161 (1.00) |
0.0447 (1.00) |
0.0182 (1.00) |
del 13q13 3 | 21 (57%) | 16 |
0.0178 (1.00) |
0.508 (1.00) |
0.176 (1.00) |
0.694 (1.00) |
1 (1.00) |
0.814 (1.00) |
1 (1.00) |
0.575 (1.00) |
del 14q11 2 | 16 (43%) | 21 |
0.00896 (1.00) |
0.746 (1.00) |
1 (1.00) |
0.211 (1.00) |
0.105 (1.00) |
0.157 (1.00) |
0.431 (1.00) |
0.0261 (1.00) |
del 14q32 31 | 19 (51%) | 18 |
0.00255 (0.449) |
1 (1.00) |
1 (1.00) |
0.127 (1.00) |
0.105 (1.00) |
0.157 (1.00) |
0.431 (1.00) |
0.0255 (1.00) |
del 15q15 1 | 14 (38%) | 23 |
0.00157 (0.279) |
1 (1.00) |
0.305 (1.00) |
0.0788 (1.00) |
1 (1.00) |
0.465 (1.00) |
1 (1.00) |
0.25 (1.00) |
del 16p13 3 | 3 (8%) | 34 |
1 (1.00) |
0.0875 (1.00) |
0.229 (1.00) |
0.479 (1.00) |
1 (1.00) |
1 (1.00) |
||
del 16q21 | 9 (24%) | 28 |
0.0239 (1.00) |
1 (1.00) |
1 (1.00) |
0.232 (1.00) |
0.664 (1.00) |
0.612 (1.00) |
0.401 (1.00) |
0.518 (1.00) |
del 16q24 1 | 11 (30%) | 26 |
0.00342 (0.596) |
0.495 (1.00) |
0.146 (1.00) |
0.752 (1.00) |
1 (1.00) |
0.76 (1.00) |
1 (1.00) |
0.74 (1.00) |
del 22q12 2 | 29 (78%) | 8 |
0.104 (1.00) |
0.109 (1.00) |
0.691 (1.00) |
1 (1.00) |
0.0532 (1.00) |
0.134 (1.00) |
0.0171 (1.00) |
0.00744 (1.00) |
P value = 0.000723 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 16 | 10 |
DEL PEAK 4(3P21.1) MUTATED | 5 | 10 |
DEL PEAK 4(3P21.1) WILD-TYPE | 11 | 0 |
P value = 2.1e-05 (Fisher's exact test), Q value = 0.0038
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 16 | 21 |
DEL PEAK 8(9P21.3) MUTATED | 16 | 7 |
DEL PEAK 8(9P21.3) WILD-TYPE | 0 | 14 |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = MESO-TP.transferedmergedcluster.txt
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Number of patients = 37
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Number of significantly focal cnvs = 23
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Number of molecular subtypes = 8
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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.