7.0 years ago by
The University of Sheffield
Ok, I found the answer by looking at the help page for the path-scan function
This is a tab-delimited file prepared from a pathway database (such as KEGG), with the columns: [pathid, pathname, class, geneline, diseases, drugs, description] The latter three columns are optional (but are available on KEGG). The geneline contains the "entrezid:genename" of all genes involved in this pathway, each separated by a "|" symbol.
For example, a line in the pathway-file would look like:
hsa00061 Fatty acid biosynthesis Lipid Metabolism 31:ACACA|32:ACACB|27349:MCAT|2194:FASN|54995:OXSM|55301:OLAH
Ensure that the gene names and entrez IDs used match those used in the MAF file. Entrez IDs are not mandatory (use a 0 if Entrez ID unknown). But if a gene name in the MAF does not match any gene name in this file, the entrez IDs are used to find a match (unless it's a 0).
It doesn't really say how to "prepare" such a file though?