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

Question

[yourA]

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

Answer 1

[Mike]

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

Answer 2

[mehran.karimzade]

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.

[yourA]

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?

[mehran.karimzade]

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

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

[yourA]

Thanks, I'll give this a try