I have a list of differentially expressed gene in a given experiment.
I would like to get an idea of 'How upstream is a gene in any of it's pathway ?'
I would ideally get an 'upstream score' ranging from 0 to 1 for each gene, 0 meaning the gene is always at the downstream of it's pathways or 1 meaning the gene is always upstream of it's pathways (master regulator).
For instance, in the MAPK signalling Pathway TGFB would have a score of 1, intermediary genes would have a score between 0 and 1, and most downstream genes such as MAX would have scores of 0.
I was thinking about using KEGG pathways and R.