On my way to read and run a pathway/gene set analysis on some microarray data, I realized that besides the fact that there are many different ways (statistical methods) to do the analysis, all of them (at least as far as I know) stays at statistic and as you already know returns a p-value or/and an enrichment score for each pathway/gene set.
Today, I was wondering if there is any approach ever implemented to do pathway analysis but to take into account also information from systems biology and not only on statistical inferences.
Such information could be the role of each gene inside the gene set, like inducer , inhibitor. Also it could be info about the topology of that specific gene set and maybe gene's inter-correlations.
Does anyone have in mind any research article on such an approach ? Any info or even idea is welcomed.