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Table 1 Summary of node (genes and pathways) color classification in the network graph visualization obtained with panev.exprnetwork() function. The upregulated genes/pathways are reported using a red scale, from light red (low) to dark red (strong). The downregulated genes/pathways are reported using a green scale, from light green (low) to dark green (strong)

From: PANEV: an R package for a pathway-based network visualization

Gene / Pathway classificationGene fold change (FC) / Pathway expression score value
low
upregulated/downregulated
< 25% of top up/downregulated
gene/pathway value
moderate
upregulated/downregulated
≥25% and < 50% of top up/downregulated
gene/pathway value
high
upregulated/downregulated
≥ 50% and < 75% of top up/downregulated
gene/pathway value
strong
upregulated/downregulated
≥ 75% of top up/downregulated
gene/pathway value