Can I submit a list of genes with their p-values from a microarray experiment instead of fold changes?
You cannot use p-values instead of fold changes. The idea is to capture the amount of change that is happening on the pathway. The p-values have to do with the ratio between the expression level and the variance with which this is measured. In essence, the p-values are influenced by the technology (affy, illumina, etc), number of replicate measurements, etc. (this paper discusses how various technologies provide very different results: http://vortex.cs.wayne.edu/papers/Tigs_article.pdf. The results of the pathway analysis should not be influenced by these factors but only by the amount of change measured for each gene (estimated as accurately as possible, whichever way you think is best). The analysis method also propagates the perturbation of the genes throughout the pathway following the topology that describes how the genes interact. If one gene A represses B immediately downstream, and if A goes up by 2 fold, B should feel this as an inhibitory influence proportional to the amount
