Genes and respective pathways from FTP database

Question

[thorwahl]

For my RNA-seq project, I have a list of genes in one column and I am trying to associate this list with a second column that has all the biological pathways that each respective gene is involved in. I looked at databases such as PathwaysCommons, but they don't seem to provide a non-network based representation that I can FTP directly into my local computer.

Is there a way to get a list of genes and their respective associated biological pathways? One gene can have many very many pathways that it is known to be involved in. Is there any online utility that I can use to find this kind of information?

[Sam]

Think you can download those information through http://www.pathwaycommons.org/pc2/downloads

The GSEA format might be the easiest to work on

Answer 1

[roy.granit]

I suggest that you try and do this by using either:

• BioMart
• DAVID

They offer a GUI that allow you to easily append pathway information to a list of genes.