Problems downloading kegg pathways

[Glorificus]

Hello,
I am new to J-express, so I don't know if I'm doing something wrong, but I cannot seem to download pathways in the "pathway analysis section". There are no pathways available to begin with.

When clicking "Download pathway" I get a window with the following information:
FTP location: ftp.genome.jp
Path to pathways. /pub/kegg/pathway_gif
Path to genes:

Available sets: (noting)
Downloaded sets: hsa

What am I doing wrong?


Kristina


P.S I see in the download path, that the files are indeed located on my C drive. Bu how to connect these to the J-express software?

[Bjarte Dysvik]

Hi,

If the pathway files are put in the correct folder (the one pecified under settings -> options ->files and folders), they should be picked up automatically by J-Express..
To use them, open the pathway analysis and select the correct pathway set in the set dropdown box.

If the set are still missing from the dropdown list, your pathway files are probably damaged by for instance an interrupted download, or J-Express does not have the permission to load them.

regards,
Bjarte

[anef]

I have the same problem.

There is nothing to select under "Pathway set", even though I have downloaded the files and they they seem to be in the correct folder.
Do you have any more suggestions?

Where on the Kegg webpage can I find Kegg IDs to download and put in my data set with ID linker, if this is the problem?

Ane

[Bjarte Dysvik]

Hi, can you give me some more information?

have you tried closing and reopening the pathway window after downloading the pathway?

What is the name of your new folder (inside the PW folder)? do you have a "genome" and "map_title.tab" file there?

regards,
Bjarte

[anef]

The name of the folder inside PW is mmu. The "genome" and "map_title.tab" files are also under PW.

It actually worked yesterday, after I had copied the files from my colleague (these files were from last October). But when I tried again today the pathways were disappeared from "Pathway set".

Yes, I also tried closing and reopening the pathway window after downloading.

Is the appearance of the pathways dependent of the selected dataset? Because I dont remember which dataset I had selected when it worked.

Ane