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 | |