This pipeline checks the correlation between cancer subtypes identified by different molecular portraits to selected clinical features.
Testing the association between 2 clustering variables and 5 clinical features across 25 samples, no significant finding detected with P value <= 0.05 and Q value <= 0.25.
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CNMF clustering analysis on mRNA expression data identified 3 subtypes that are not correlated to any clinical features.
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3 subtypes identified in current cancer cohort by 'mRNA HierClus consensus subtypes'. These subtypes are not correlated to any clinical features.
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No gene mutations related to clinical features.
Clinical Features |
mRNA CNMF subtypes |
mRNA HierClus consensus subtypes |
|
Time to Death | survival |
0.274 (1.00) |
0.315 (1.00) |
AGE | continuous |
0.666 (1.00) |
0.635 (1.00) |
GENDER | binary |
0.562 (1.00) |
0.817 (1.00) |
PATHOLOGY T | binary |
0.296 (1.00) |
0.256 (1.00) |
PATHOLOGY N | multiclass(3) |
0.35 (1.00) |
0.349 (1.00) |
Cluster Labels | 1 | 2 | 3 |
Number of samples | 13 | 8 | 4 |
P value = 0.274 (Kaplan-Meier), Q value = 1
N | nEvent | Duration Range (Median), Month | |
ALL | 22 | 2 | 0.5 - 56.8 (13.2) |
subtype1 | 10 | 0 | 6.0 - 56.8 (8.2) |
subtype2 | 8 | 1 | 0.5 - 37.0 (8.9) |
subtype3 | 4 | 1 | 20.6 - 45.2 (38.9) |
P value = 0.666 (ANOVA), Q value = 1
nSamples | Mean (Std.Dev) | |
ALL | 25 | 64.2 (10.0) |
subtype1 | 13 | 63.8 (11.1) |
subtype2 | 8 | 62.6 (9.1) |
subtype3 | 4 | 68.2 (9.2) |
P value = 0.562 (Chi-square), Q value = 1
nSamples | FEMALE | MALE |
ALL | 12 | 13 |
subtype1 | 5 | 8 |
subtype2 | 5 | 3 |
subtype3 | 2 | 2 |
P value = 0.296 (Chi-square), Q value = 1
nSamples | T1 | T2+T3 |
ALL | 8 | 16 |
subtype1 | 5 | 7 |
subtype2 | 3 | 5 |
subtype3 | 0 | 4 |
P value = 0.35 (Chi-square), Q value = 1
nSamples | N0 | N1 | N2 |
ALL | 15 | 4 | 4 |
subtype1 | 9 | 2 | 1 |
subtype2 | 5 | 1 | 1 |
subtype3 | 1 | 1 | 2 |
Cluster Labels | 1 | 2 | 3 |
Number of samples | 4 | 9 | 12 |
P value = 0.315 (Kaplan-Meier), Q value = 1
N | nEvent | Duration Range (Median), Month | |
ALL | 22 | 2 | 0.5 - 56.8 (13.2) |
subtype1 | 4 | 1 | 20.6 - 45.2 (38.9) |
subtype2 | 9 | 1 | 0.5 - 37.0 (13.2) |
subtype3 | 9 | 0 | 6.0 - 56.8 (8.1) |
P value = 0.635 (ANOVA), Q value = 1
nSamples | Mean (Std.Dev) | |
ALL | 25 | 64.2 (10.0) |
subtype1 | 4 | 68.2 (9.2) |
subtype2 | 9 | 62.3 (8.5) |
subtype3 | 12 | 64.2 (11.5) |
P value = 0.817 (Chi-square), Q value = 1
nSamples | FEMALE | MALE |
ALL | 12 | 13 |
subtype1 | 2 | 2 |
subtype2 | 5 | 4 |
subtype3 | 5 | 7 |
P value = 0.256 (Chi-square), Q value = 1
nSamples | T1 | T2+T3 |
ALL | 8 | 16 |
subtype1 | 0 | 4 |
subtype2 | 3 | 6 |
subtype3 | 5 | 6 |
P value = 0.349 (Chi-square), Q value = 1
nSamples | N0 | N1 | N2 |
ALL | 15 | 4 | 4 |
subtype1 | 1 | 1 | 2 |
subtype2 | 6 | 1 | 1 |
subtype3 | 8 | 2 | 1 |
Input Data
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Cluster data file = LUAD.mergedcluster.txt
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Clinical data file = LUAD.clin.merged.picked.txt
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Number of samples = 25
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Number of clustering variables = 2
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Number of filtered clinical features = 5
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Minimum size criteria to remove small clusters = 3