Fig. 1: CARNIVAL pipeline. | npj Systems Biology and Applications

Fig. 1: CARNIVAL pipeline.

From: From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL

Fig. 1: CARNIVAL pipeline.

The CARNIVAL pipeline requires as input a prior knowledge network and differential gene expression. The information on perturbed targets and their effects can be assigned (Standard CARNIVAL “StdCARNIVAL”) or omitted (InvCARNIVAL). The differential gene expression is used to infer transcription factor (TF) activities with DoRothEA, which are subsequently discretized in order to formulate ILPconstraints. As a result, CARNIVAL derives a family of highest scoring networks which best explain theinferred TF activities. Continuous pathway and TF activities can be additionally considered in the objective function

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