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Table 2 HCC – Silhouette scores based on PCA transform applied to scores of subnetworks reported as significantly differentially expressed by PFSNet and SPSNet

From: SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data

 

Normal vs HCC

Normal vs HCC

 

(first 3 PCs, with batch labels)

(2nd, 3rd PC, without batch labels)

PFSNet

0.145

0.117

SPSNet

0.268

0.298

  1. SPSNet leads to better separation (silhouette scores marked in bold) between normal/HCC phenotypes, as well as the two different batches