Introducing PCApp and GRN App

Welcome to PCApp and GRN App !

PCApp determines if your tumor samples show activation of the gene regulatory network ‘GRN’ (figure 1 on the right).
GRN App predicts the network dynamics and assesses the impact of each component of the network on the expression of the other network members.

How to proceed with PCApp?
Download a demo file here. A source file template is available here; please complete it as described here and analyze your tumor samples in the appropriate cohort: hepatocellular carcinoma, cholangiocarcinoma, colorectal carcinoma, or stomach and esophageal carcinoma. You can download the figure (Factor Map) or an excel sheet containing all the active samples as well as their "activation index".

Click here for a tutorial of PCApp.

Figure 1 - Gene Regulatory Network



How to interprete PCApp results?
PCApp positions your samples (bold blue dots) in a two dimensional Principal Component Analysis plot that already incorporates normal and tumor samples of the appropriate cohort from the TCGA database. PCApp also defines an activation index of the network in your sample which is maximum if the position of your sample fits with the center of the tumor samples of the TCGA cohort, and minimum if your sample fits with the center of the normal samples of the TCGA cohort.

How to proceed with GRN App?
Click here for a tutorial of GRN App.
You can download GRN App here :