SPIA - How to update and integrate new KEGG pathways????

Question: SPIA - How to update and integrate new KEGG pathways????

4.4 years ago by

yourA • 20

United Kingdom

yourA • 20 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 • 1.8k views

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modified 17 months ago by Mike • 0 • written 4.4 years ago by yourA • 20

4.4 years ago by

mehran.karimzade • 180

Canada

mehran.karimzade • 180 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 COMMENT • link modified 3 months ago by RamRS ♦ 25k • written 4.4 years ago by mehran.karimzade • 180

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 REPLY • link written 4.4 years ago by yourA • 20

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

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

ADD REPLY • link written 4.4 years ago by mehran.karimzade • 180

Thanks, I'll give this a try

ADD REPLY • link written 4.3 years ago by yourA • 20

17 months ago by

Mike • 0

University of Cincinnati

Mike • 0 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 COMMENT • link modified 17 months ago by EagleEye ♦ 6.6k • written 17 months ago by Mike • 0

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