kegg for arabidopsis

[Tong-Chen]

Thanks for this great tool for enrichment analysis.

I have successfully used clusterprofile to perform GO and KEGG analysis given human entrez ids.

However, for Arabidopsis, I have encountered a problem with bitr_kegg when transferring IDs to seach for help. 100% of these IDs are failed to map.

Ps. When using these entrez IDs for GO enrichment, no warning message encounted, assuming 100% map.

> library(DOSE)

DOSE v3.0.10  For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

> library(clusterProfiler)
clusterProfiler v3.2.11  For help: https://guangchuangyu.github.io/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu., Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
> entrez_id <- "829795
+ 835540
+ 832343
+ 821775
+ 832491
+ 840522
+ 831161
+ 816328
+ 821280
+ 5008021
+ 830796
+ 814939
+ 843695
+ 820034
+ 824647
+ 830562
+ 821194
+ 840271
+ 830561
+ 838464"
> entrez_id <- read.table(text=entrez_id)
> entrez_id
        V1
1   829795
2   835540
3   832343
4   821775
5   832491
6   840522
7   831161
8   816328
9   821280
10 5008021
11  830796
12  814939
13  843695
14  820034
15  824647
16  830562
17  821194
18  840271
19  830561
20  838464

> bitr_kegg(entrez_id, fromType='kegg', toType='uniprot', organism="ath")
[1] kegg    uniprot
<0 line> (or 0 row.names)
Warning message:
In bitr_kegg(entrez_id, fromType = "kegg", toType = "uniprot", organism = "ath") :
  100% of input gene IDs are fail to map...

> bitr_kegg(entrez_id, fromType='ncbi-geneid', toType='kegg', organism="ath")
[1] ncbi-geneid kegg       
<0> (0 row.names)
Warning message:
In bitr_kegg(entrez_id, fromType = "ncbi-geneid", toType = "kegg",  :
  100% of input gene IDs are fail to map...

> kk <- enrichKEGG(id, organism="ath", keyType='uniprot', pvalueCutoff=0.01,
                                pAdjustMethod="BH", qvalueCutoff=0.1)

Tong Chen

[GuangchuangYu]

pls follow https://guangchuangyu.github.io/clusterProfiler/#feedback and post your question to the forum.

[GuangchuangYu]

answered in https://support.bioconductor.org/p/93170/#93171.