Hi to all and thanks for the eventual answers I used many time Ingenuity(IPA) for multi omics data integration What interested me in IPA compared to other bioinformatic tools (string or david) was that IPA consider the gene/protein fold changes in the interpratation of pathway activation. For example a protein downregulation could activate a pathway. Many time I saw people that split the downregulated gene from the upregulated then they perform two separated pathway analyses to find upregulated and downregulated pathways with the simplistic assumption that upregulation reflect always a pathway upregulation. Does exist a cytoscape plugin allowing to infer on pathway activation/repression considering the real effects of protein up/down regulations? thanks
