This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 2 different clustering approaches and 2 clinical features across 24 patients, no significant finding detected with P value < 0.05.
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CNMF clustering analysis on sequencing-based miR expression data identified 2 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 2 subtypes that do not correlate to any clinical features.
Clinical Features |
VITALSTATUS | GENDER |
Statistical Tests | Fisher's exact test | Fisher's exact test |
MIRseq CNMF subtypes | 0.675 | 0.0803 |
MIRseq cHierClus subtypes | 0.675 | 0.0803 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 9 | 15 |
P value = 0.675 (Fisher's exact test)
nPatients | Class0 | Class1 |
---|---|---|
ALL | 11 | 13 |
subtype1 | 5 | 4 |
subtype2 | 6 | 9 |
P value = 0.0803 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 9 |
subtype1 | 8 | 1 |
subtype2 | 7 | 8 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 15 | 9 |
P value = 0.675 (Fisher's exact test)
nPatients | Class0 | Class1 |
---|---|---|
ALL | 11 | 13 |
subtype1 | 6 | 9 |
subtype2 | 5 | 4 |
P value = 0.0803 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 9 |
subtype1 | 7 | 8 |
subtype2 | 8 | 1 |
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Cluster data file = LIHC.mergedcluster.txt
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Clinical data file = LIHC.clin.merged.picked.txt
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Number of patients = 24
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Number of clustering approaches = 2
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Number of selected clinical features = 2
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Exclude small clusters that include fewer than K patients, K = 3
consensus non-negative matrix factorization clustering approach (Brunet et al. 2004)
Resampling-based clustering method (Monti et al. 2003)
For binary clinical features, two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
This is an experimental feature. Location of data archives could not be determined.