No enriched GO terms with 1000 more genes
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Ruixuan ▴ 10
@ruixuan-23626
Last seen 11 months ago
Kyoto University

Hi everyone, I'm doing a GO analysis after finish the statistical test by edgeR.

Before, I did the comparison between group1 vs group2, group1 vs group3, group1 vs group4.

Here the problem came when I compared group1 vs group4, there are 1740 genes showing to be significantly overrepresented in group 4. However, when I used the code below

enrich.go.BP = enrichGO(gene = up_gene.4vs1$GeneID, OrgDb = Acan.OrgDb, keyType = "ENTREZID", ont = "BP", pvalueCutoff = 0.01, qvalueCutoff = 0.05, readable = T)  There is no enriched terms in the result. This code worked well when I compared other groups to group1, so I think there may be no problem on code. Thus, I'm wondering why I got this result? How can I fix it? Is it that I got too many genes which locate in almost all kinds of category so that there is no statistical significant enriched terms? Thank you in advance. Edited: 2020-06-11 Thanks to the comment by Kevin Blighe. I will show more information below. The Acan.OrgDb is the one I loaded by using Annotationhub, because my target species "acanthamoeba castellanii" is not a model organism. hub <- AnnotationHub::AnnotationHub() amoeba <- query(hub, "Acanthamoeba castellanii") # title # AH65301 | Acanthamoeba castellanii str. Neff transcript information # AH73987 | Transcript information for Acanthamoeba castellanii str Neff # AH74626 | Transcript information for Acanthamoeba castellanii str Neff # AH81410 | org.Acanthamoeba_castellanii_Neff_strain.eg.sqlite # AH81411 | org.Acanthamoeba_castellanii_str._Neff.eg.sqlite # AH81412 | org.Acanthamoeba_castellanii_strain_Neff.eg.sqlite  Here I chose the AH81410 because its Db type is OrgDb. Acan.OrgDb <- hub[["AH81410"]] > Acan.OrgDb OrgDb object: | DBSCHEMAVERSION: 2.1 | DBSCHEMA: NOSCHEMA_DB | ORGANISM: Acanthamoeba castellanii_Neff_strain | SPECIES: Acanthamoeba castellanii_Neff_strain | CENTRALID: GID | Taxonomy ID: 1257118 | Db type: OrgDb | Supporting package: AnnotationDbi  And from colnames(Acan.OrgDb), we could see that it supported ENTREZID. > columns(Acan.OrgDb) [1] "ACCNUM" "ALIAS" "CHR" "ENTREZID" "EVIDENCE" "EVIDENCEALL" "GENENAME" "GID" "GO" "GOALL" [11] "ONTOLOGY" "ONTOLOGYALL" "PMID" "REFSEQ" "SYMBOL"  Then, I prepared my significant genes list into ENTREZID format. The format is generated by combining ORFID, locus_tag and annotation from files downloaded from NCBI. Here, the GeneID is recording those id in ENTREZID format. >up_gene.4vs1 Locus_tag ORFID Name Accession Start Stop Strand GeneID Locus Protein_product Length Protein_Name 1 ACA1_000790 gene5490 Un NW_004457578.1 5136 5699 + 14921342 NA XP_004343320.1 187 hypothetical protein ACA1_000790 2 ACA1_001250 gene2057 Un NW_004457658.1 4004 11317 + 14924768 NA XP_004353303.1 1925 hypothetical protein ACA1_001250 3 ACA1_001280 gene2060 Un NW_004457658.1 17392 18733 - 14924773 NA XP_004353305.1 258 hypothetical protein ACA1_001280 4 ACA1_001300 gene2062 Un NW_004457658.1 20701 23681 - 14924770 NA XP_004353306.1 599 fucose1-phosphate guanylyltransferase  You may also notice that there are hypothetical proteins which could blur the prediction. Although there are 691 entries of hypothetical protein, there are still (1049/1740) entries left. Thus, I'm a little bit confused about the results from enrichGO showing no enriched GO terms. type(up_gene.4vs1) # [1] "character" type(up_gene.4vs1$GeneID)
# [1] "integer"


clusterprofiler GO • 200 views
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Hi, you need to help us so that we can properly diagnose the problem. For example, you need to show what are the contents of up_gene.4vs1$GeneID. Also, how did you load or install Acan.OrgDb? Thank you. ADD REPLY 0 Entering edit mode Thank you. I have edited my question. ADD REPLY 0 Entering edit mode How is up_gene.4vs1$GeneID encoded? - as a factor?; are the IDs definitely Entrez IDs?

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Thanks for your comment. The type is integer and I checked some GeneID directly by this page (Protein Table for Acanthamoeba castellanii str. Neff). It seems no problem here.

https://www.ncbi.nlm.nih.gov/genome/browse/#!/proteins/278/28653%7CAcanthamoeba%20castellanii%20str.%20Neff/14917167

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