I have been trying to analyse transcriptome data with SPIA package. The output gives me a list of 10 significant pathways with the status activated or Inhibited.
I was wondering if someone could explain these terms in status of pathway more clearly ? These can have very varied meaning if I present the results in front of a molecular biology or functional genomics audience. The log2FC values of genes does not seem to correspond very much with the status of that pathway.