Enrichment analysis based on kegg for zebrafish

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

kegg enrichment clusterprofiler r

• 1,551 views • link

written 3.4 years ago by PBC •

I am unsure what is happening. The IDs that you post are NCBI gene IDs (Entrez IDs) and should be mappable via enrichKegg():

require(org.Dr.eg.db)
head(mapIds(org.Dr.eg.db, keys = gene, keytype = 'ENTREZID', column = 'SYMBOL'))
'select()' returned 1:1 mapping between keys and columns
          108179356              562008           101886804           100007552
     "LOC108179356"            "cyp4v7" "si:cabz01112025.1"           "ifi44a5"
          110437771              561067
     "LOC110437771"               "mxf"

Have you posted this as an issue on the clusterProfiler GitHub page?

• 0 views • link

written 3.4 years ago by Kevin Blighe

Thank you Kevin for your answer!

Yes, I contact the author on github page. He replied by saying that it was fix in the latest version on the github (https://github.com/YuLab-SMU/clusterProfiler/issues/546). So, by using the version provied on github it works.

Again, many thanks for your answer!

• 0 views • link

written 3.4 years ago by PBC •

0 answers

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