Table 3 Comparison of PathME vs conventional sNMF consensus clustering of individual omics features in terms of cophenetic correlation and silhouette index
Cancer datasets | Cophenetic correlation | Consensus silhouette | |||
|---|---|---|---|---|---|
Disease | Omics type | PathME | sNMF (ind. features) | PathME | sNMF (ind. features) |
CRC (5 clusters) | mRNA | 1 | 1 | 0.99 | 0.87 |
miRNA | 1 | 1 | 0.97 | 0 | |
CNV | 1 | 0.99 | 0.99 | 0.93 | |
GBM (4 clusters) | mRNA | 1 | 0.99 | 1 | 1 |
miRNA | 1 | 1 | 0.93 | 0.86 | |
Methylation | 1 | 1 | 1 | 1 | |
LSCC (4 clusters) | mRNA | 0.92 | 1 | 0.67 | 1.00 |
miRNA | 1 | 1 | 0.98 | 0.98 | |
Methylation | 1 | 0.99 | 1.00 | 0.97 | |
BRCA (5 clusters) | mRNA | 0.98 | 0.99 | 0.88 | 0.94 |
miRNA | 1 | 0.91 | 0.99 | 0.49 | |
CNV | 1 | 1 | 1 | 1 | |