[not working] Enrichment analysis based on kegg for zebrafish

[paolabc]

Hello There!

I am doing the enrichment analysis based on kegg. The analysis is based on zebrafish entrezid/ncbi-geneid

Clusterprofiler seems to work for this example

data(geneList, package='DOSE')
de <- names(geneList)[1:100]
yy <- enrichKEGG(de, pvalueCutoff=0.01)
head(yy)

But when I tried my code, it does not work. I did it for my whole dataframe and then I tried also to do it a small vector.
Here is the code that I treid with this small vector

gene<-c("108179356","562008","101886804","100007552","110437771","561067","108182459","100331916","101885332","564515",
          "103910768","641469","100149422","101887060","100332327","110440209","101884367","100321135","101884831","110438346","100330864","568416","791732","100333496","103910561","100033600","100535845","564958","101885505","100003496",
          "101886822","561322","100150906","110437767","100537716","101883600","100534958","100334351","100334396","110439967","108180085","100126129","103910381","751636","558010","402956","110438542","445250","140426","103909751",
          "101883443","606720","101885018","767650","794549","100333562","100329648","101883749","30491","565074",
          "572000","541341","101886406","569265","110439426","100536937","568476","101885577","393642","100073325",
          "334527","569700","100126810","108179091","103910871","563246","553303","767727","321786","100101643",
          "100331412","406525","393877","100124605","404607","100142642","571832","101884972","560315","110437923",
       "100006428","100333322","797319","100534706","101886995","403048","558563","100334085","110439304","110438375",
          "541495","100001581","751644","799405","550161","101886862","100536995","100322009","493600","570947",
          "792293","101883651","101887154","100150732","108191751","100003113","798168","322609","555340","325226",
          "449647","323922","100535070","100149562","100334245","100320750","568060","555985","336124","569908",
          "796658","564701","100151323","100332814","103911451","555875","402973","559162","100333484","570258",
          "564395","557566","567867","100535820","368924","572146","110439111","100330358","100333826","100329818",
          "386638","108180146","100333352","792676","751624","334459","110439911","393606","100332028","572463",
          "557996","327143","100334248", "561095","553318","561893","554013","556081","563670","192312", 
          "795788","64608", "562208","555764","567288","100000570", "100037374", "555703","100333916", "436710", 
          "768186","406756","559809","559447","386801","558800","100538153", "323926","334474","338317", 
          "554016","436734","393260","170455","406416","792610","436793","101886789", "563011","767805", 
          "553505","553371","569489","30715", "565037","323679","606585","562742","553243","553451", 
          "559643","100034609", "557451","571383","100002795" ,"100000256" ,"796163","793727","100334879" ,"325402", 
          "566102","555285","798791","100535772" ,"566728","100033647", "559928","110438638" ,"563017","393777", 
          "560549","108191970" ,"266799","100332164","360150","407708","100000165", "334561","100007362", "572187", 
          "565952","550239","559976","550436","563876","565434","562999","793823","562076","336984", 
          "567731","100332125" ,"404211","445133","566695","559457","560418","445026","101882648", "492364", 
          "560639","561921","323181","406519","81590", "415203","794108","791150","566146","571441")
mf <- enrichKEGG(gene, organism = "dre",keyType = 'ncbi-geneid')

The message that I received for this result and also for my whole dataset.
--> No gene can be mapped....
--> Expected input gene ID:
--> return NULL.

What could be the reason for it?

Besides, I am sure also that my entrezids in my whole dataset are character objects and they are not considered as numbers. Since entrezid are only numbers, it could be interepreted in this way.

Thank you in advance for taking this time

[yangxinzhi]

I ran into the same problem when I used the same data with this package and kobas analysis and got completely different results. Yesterday it was shown that no genes were able to map, today it is shown that no single pathway is significant. I checked my id number carefully and there is no problem.

[paolabc]

Hello There!

I also tried some minutes ago Kobas analysis, and it worked there. I do not know why errors is happening on ClusterProfiler kegg enrichmnet.

By the way, I also searched for some answers. I found this poster from some years ago ( link : https://www.biostars.org/p/305258/#9556298) . The wangchangliang0209's answer was that it is possible that for other animal, diregard humans, it need another input. So far, I tried "dre_102725537,dre_795613,dre_393541,dre_100000710,dre_325037,dre_558156" and "DRE_102725537,DRE_795613,DRE_393541,DRE_100000710,DRE_325037,DRE_558156". Both did not work for me.

Besides, I tried enrichMKEGG and my input worked. So it might be something with enrichKEGG function.

[yangxinzhi]

So we should use enrichMKEGG ?

[huerqiang]

Already soved by the Github version of clusterProfiler.

[guidohooiveld]

.... and install the Github version for example through:

remotes::install_github("YuLab-SMU/clusterProfiler").

Current Github version is v4.7.1.

@paolabc: it then worked using your 'small vector', although only with 'relaxed' significance cutoff values gene sets are identified.

> mf <- enrichKEGG(gene, organism = "dre",keyType = 'ncbi-geneid',  pvalueCutoff=0.9, qvalueCutoff=1)
> mf
#
# over-representation test
#
#...@organism    dre 
#...@ontology    KEGG 
#...@keytype     ncbi-geneid 
#...@gene        chr [1:270] "108179356" "562008" "101886804" "100007552" "110437771" ...
#...pvalues adjusted by 'BH' with cutoff <0.9 
#...68 enriched terms found
'data.frame':   68 obs. of  9 variables:
 $ ID         : chr  "dre05168" "dre04012" "dre00260" "dre04216" ...
 $ Description: chr  "Herpes simplex virus 1 infection - Danio rerio (zebrafish)" "ErbB signaling pathway - Danio rerio (zebrafish)" "Glycine, serine and threonine metabolism - Danio rerio (zebrafish)" "Ferroptosis - Danio rerio (zebrafish)" ...
 $ GeneRatio  : chr  "6/47" "4/47" "2/47" "2/47" ...
 $ BgRatio    : chr  "204/7000" "110/7000" "47/7000" "62/7000" ...
 $ pvalue     : num  0.00226 0.00613 0.03939 0.0647 0.07409 ...
 $ p.adjust   : num  0.156 0.211 0.489 0.489 0.489 ...
 $ qvalue     : num  0.156 0.211 0.489 0.489 0.489 ...
 $ geneID     : chr  "30491/565074/30715/323679/560549/404211" "560549/550436/404211/492364" "64608/266799" "100006428/334561" ...
 $ Count      : int  6 4 2 2 2 3 2 1 3 3 ...
#...Citation
 T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.
 clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.
 The Innovation. 2021, 2(3):100141 

> 
> packageVersion("clusterProfiler")
[1] ‘4.7.1’
> 

[paolabc]

Thank you all for your support.! The installation from GitHub solved my issue.