clusterprofiler KEGG enrichment for arabidopsis
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@chentong_biology-9142
Last seen 4.6 years ago
China

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. 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)$V1
> entrez_id
[1]  829795  835540  832343  821775  832491  840522  831161  816328  821280 5008021  830796
> bitr_kegg(entrez_id, fromType='kegg', toType='uniprot', organism="ath")
[1] kegg    uniprot
<0 行> (或0-长度的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="uniprot", organism='ath')
   ncbi-geneid    uniprot
1       840522     F4I1L3
2       816328     Q9SI16
3      5008021     Q9LIE8
4       829795 A0A178V4B3
5       829795     O23237
6       831161     Q9LYV5
7       832343 A0A178U9H3
8       832343     Q9FFC7
9       832491     Q9FNF8
10      835540     F4K0D3
Warning message:
In bitr_kegg(entrez_id, fromType = "ncbi-geneid", toType = "uniprot",  :
  27.27% of input gene IDs are fail to map...

> bitr_kegg(entrez_id, fromType="ncbi-geneid", toType="kegg", organism='ath')
[1] ncbi-geneid kegg       
<0 行> (或0-长度的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)

Edit1: transfer dataframe to vector to exclude R usage problem.

 

Thanks!

 

Tong Chen

clusterprofiler • 1.5k views
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Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…
bitr_kegg(as.character(entrez_id[,1]), fromType='ncbi-geneid', toType='kegg', organism="ath")

should work.

see:

> bitr_kegg("829795", fromType="ncbi-geneid", toType="uniprot", organism='ath')
  ncbi-geneid    uniprot
1      829795 A0A178V4B3
2      829795     O23237
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Thans Guangchuang for your quick answers. First sorry for the mis-uasge of dataframe and vector. It should not be a question here. Second, transferring 'ncbi-geneid' to 'uniprot' works (I can use enrichKEGG with uniprot id now), but 'ncbi-geneid' to 'kegg' return no mapping. Please help check again. Thank you! 

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Entering edit mode

fixed in version >=3.2.13.

 

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Thanks! Sorry for late response.This 'Add Reply' link does not work well all time in China mainland due to the usage of google site java library.

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