hi i have a question regarding pathway analysis from RNA-SEQ data.
From what i understand, if the data states that a particular pathway is enriched, it i suggesting that there is increased/decreased activity of that pathway since the genes (proteins) making up the pathway cascade is differentially expressed. But from my understanding, generally when one talk about pathway activation, it mainly involves phosphorylation levels of the proteins in that pathway that alters activity. That is whether a pathway is activated or not mainly involves phosphorylation of proteins, not so much about the expression level of the protein. How reliable is it then that pathway analysis from rna-seq data can be used to suggest the activity of a particular pathway?