Am I right that pathways in KEGG do not have a direction? What I mean by that is for example pathway "KEGG_APOPTOSIS" contains genes that can activate or down regulate apoptosis in cell, am I right? Or is it only those that can activate? What about Reactome/wikipathways?
For KEGG, the whole pathway per se doesn't have a "direction", but when known, the effects of individual genes (activation, inhibition, and so forth) are shown. See Notation on the KEGG Pathway Map help page.
I suppose the same is true for Reactome and WikiPathways, including using a similar notation. See, for example, the Apoptosis pathway at WikiPathways (which, coincidentally, was Today's Featured Pathway).