KEGG analysis for plasmodium
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MOHAMMAD • 0
@MOHAMMAD-24781
Last seen 7 months ago

I am trying to do KEGG analysis and I could not find the pathway data for Plasmodium falciparum in the gage package

data(kegg.sets.hs)

data(go.sets.hs)

data(carta.hs)

data(kegg.sets.mm)

data(go.sets.mm)

data(kegg.sets.rn)

data(go.sets.rn)

data(kegg.sets.sc)

data(go.sets.sc)

is there any package to provide me with relevant data for plasmodium

KEGG gage gageData pathview • 438 views
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 3 months ago
United States

In gage package, you need to use function kegg.gsets() to generate gene set data:

library(gage)
kg.pfa=kegg.gsets("pfa")
kegg.gs=kg.pfa$kg.sets[kg.pfa$sigmet.idx]

note the species is pfa. pfd is not one of the 6833 species currently supported by kegg.gsets(). It is likely a recent addition to KEGG. You need to add it to korg data manually using something like:

pfd.info=c("T01051", "57267", "pfd",    "Plasmodium falciparum Dd2", "", "0", "PFDG_03934", NA, NA, NA)
data(korg)
korg=rbind(korg, pfd.info)
kg.pfd=kegg.gsets("pfd")
kegg.gs=kg.pfd$kg.sets[kg.pfd$sigmet.idx]
head(kegg.gs, 3)

note that the gene IDs look like: "PFDG_00033" "PFDG_00121" etc. make sure you are using the same type of gene ID in your expression data.

you may also try our new package SBGNview for many more pathways beyond KEGG:
GitHub
https://github.com/datapplab/SBGNview
BioC
https://bioconductor.org/packages/SBGNview/

HTHs.

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shepherl 2.8k
@lshep
Last seen 16 hours ago
United States

Have you tried the KEGGREST package? It seems like there is some information for the desired organism in there

library(KEGGREST)
> org <- keggList("organism")
> org[grep(org[,"species"], pattern="falciparum"),]
     T.number organism species                    
[1,] "T00095" "pfa"    "Plasmodium falciparum 3D7"
[2,] "T01051" "pfd"    "Plasmodium falciparum Dd2"
[3,] "T01052" "pfh"    "Plasmodium falciparum HB3"
     phylogeny                                     
[1,] "Eukaryotes;Protists;Alveolates;Apicomplexans"
[2,] "Eukaryotes;Protists;Alveolates;Apicomplexans"
[3,] "Eukaryotes;Protists;Alveolates;Apicomplexans"
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I am afraid that I am a beginner in R

How to upload "Plasmodium falciparum Dd2" data?

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Check out the KEGGREST vignette for information on how to use the package. Found here: https://bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.html

I haven't used this package much so I encourage you to check out the package vignette and documentation but I think to get the pathways you could do something like keggLink("pathway", "pfd")

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Steve ▴ 10
@steve-25004
Last seen 7 months ago

The stringDB package has GO-Term, KEGG and other enrichment analysis available for Plasmodium falciparum

https://bioconductor.org/packages/release/bioc/html/STRINGdb.html

You can also try the web-based g:profiler

https://biit.cs.ut.ee/gprofiler/gost

Plasmodium falciparum is available as organism for GO, KEGG, ... enrichment there, too.

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