Question: SPIA - How to update and integrate new KEGG pathways????
0
gravatar for yourA
3.5 years ago by
yourA20
United Kingdom
yourA20 wrote:

Hi everyone,

I'm using SPIA to analyse a list of deferentially methylated genes. Does anyone know how I can update the KEGG pathways as I currently only have 137 and from what I can tell there are around 299. I know that KEGG now charges for  FTP but is there an alternative free update. I think SPIA is capable of downloading individual pathways but this would be a pretty big job to do manually. I've found these posts but can''t seem to get it to work.

 

https://support.bioconductor.org/p/51142/

https://support.bioconductor.org/p/70223/

 

So basically, can I update KEGG pathways and how do I integrate this into SPIA.

Thanks.

kegg spia • 1.5k views
ADD COMMENTlink modified 6 months ago by Mike0 • written 3.5 years ago by yourA20
0
gravatar for mehran.karimzade
3.5 years ago by
Canada
mehran.karimzade150 wrote:

You need to download the xml format of KEGG from the KEGG FTP which is not free. That is the only format SPIA uses.

Even then I had the same issue and the author of SPIA told me that only certain pathways are qualified as "Signaling Pathway" and others will not be included.

 

ADD COMMENTlink written 3.5 years ago by mehran.karimzade150

Do you have any idea what pathway analysis method has the most up to date version or would a method that utilizes biocarta etc be more reliable?

ADD REPLYlink written 3.5 years ago by yourA20

GprofileR to my knowledge uses the most up to date KEGG, Reactome, GO and etc. pathway analysis

http://biit.cs.ut.ee/gprofiler/

ADD REPLYlink written 3.5 years ago by mehran.karimzade150

Thanks, I'll give this a try

ADD REPLYlink written 3.5 years ago by yourA20
0
gravatar for Mike
6 months ago by
Mike0
University of Cincinnati
Mike0 wrote:

Late reply, but I ran into this problem a couple of days ago and found this simple bash loop on some site that will grab all the KEGG XML files for a specified species (T01001 here). You can then run the makeSPIAdata function to have SPIA process the download files.

curl "http://rest.kegg.jp/list/pathway/T01001" | cut -f 1 | while read A ; do curl -o "${A}.xml" "http://rest.kegg.jp/get/${A}/kgml" ; done
ADD COMMENTlink modified 6 months ago by EagleEye6.2k • written 6 months ago by Mike0
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