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In KEGG pathway, genes can be colored by Fold change and p-value etc, how are the gene statistics calculated?

For Gene set enrichment analysis, only genes from the input data node (filtered gene list) will be colored in the KEGG pathway gene network, using the statistics in the data node.

During GSEA (or Gene set ANOVA) computation, we also perform ANOVA on each gene based on the attributed selected independent from GESA computation (at gene set level). The results of ANOVA is only used to color the genes in the KEGG gene network. If GSEA is computed using another other database, e.g. GO, we don't compute ANOVA on each gene since GO databased doesn't have gene network information.

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