what the first column of biocyc input? refseq id or something else?

Question

[wuzongze001]

I want to map my file,which contains refseq id and expression level, to biocyc. when I go to the biocyc web(http://biocyc.org/overviewsWeb/celOv.shtml) and try to upload my data,it says the first column should be gene name or identifiers. But in its sample files(http://pathway.yeastgenome.org/expr-examples/sample.dat) the first column is like "b0003".

what is the id? how to map refseq id to this id?

Answer 1

[djinnome]

In general, the cellular overview will attempt to map the values in the first column to a unique identifier that it can find in the organism-specific biocyc database. Depending on your organism, if you have refseq ids, that might work just fine. You can learn which ids are supported for your organism by clicking on the Gene page. Any one of Accession number, gene name, Frame ID, enzyme name, or unification link will work.

In the sample file you linked to, 'b0003' is a "blattner number" that is specific to E. coli. Which organism are you working with?