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

ADD COMMENTlink 4.3 years ago yourA • 20
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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 4.3 years ago mehran.karimzade • 160
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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 4.3 years ago
yourA
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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 4.3 years ago
mehran.karimzade
• 160
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Thanks, I'll give this a try

ADD REPLYlink 4.3 years ago
yourA
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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 16 months ago Mike • 0

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