For biologists using microarrays or sequencing one of the most intersting things is finding if a pathway related to a function is activated or not. To know if a pathway is activated or not usually we need to compare the same pathway in two conditions. It means a subject centered functional scoring method. Which in turns assumes that a pathway is conserved among people and time. In addition the assumption that is done is that more expression of more genes of a pathways imply an increase of the metabolism of that pathway, which might not be true. Given that pathway has 5 genes, and that all of them are positive regulated implies that a pathway is activated? I have to dive to the origins of this, and see if there is some other way to measure how active a pathway is.