Question: In enrichGO, BP subontology doesn't work, but CC ontology does?
0
gravatar for cthangav
4 weeks ago by
cthangav0
cthangav0 wrote:

I have been following this tutorial: Introduction to ChIP-Seq using high-performance computing Tutorial.

However my dataset is for mouse not human, so I am using the following mouse databases: TxDb.Mmusculus.UCSC.mm10.knownGene, EnsDb.Mmusculus.v79, and org.Mm.eg.db.

Here is the code I used:

ego <- enrichGO(gene = entrez, keyType = "ENTREZID", OrgDb = org.Mm.eg.db, ont = "BP", pAdjustMethod = "BH", qvalueCutoff = 0.05, readable = TRUE)

When I use this enrichGO command to find enriched genes, I get "0 enriched genes found". If I view ego, I get:

> ego
# over-representation test
#
#...@organism    Mus musculus
#...@ontology    BP 
#...@keytype     ENTREZID
#...@gene    chr [1:191] "50790" "17954" "23963" "107376" "66673" "546723" "17254" ...
#...pvalues adjusted by 'BH' with cutoff <0.05
#...0 enriched terms found
#...Citation

The ego term looks like this in R studio: Ego in R studio Screenshot

When I change 'ont' argument to CC, it works. Ideally I'd like to get BP to work, as those are the terms I need.

The object entrez (which I used enrichGO on) contains these Gene IDs (which are tab delimited in the object):

> entrez 
"50790""17954""17954""17954""17954""23963""23963""107376""107376""66673""66673""546723""546723""546723""546723""17254""17254""17254""17254""17254""23825""23825""23825""23825""14870""14870""14870""110796""328953""328953""328953""328953""70640""70640""78199""78199""78199""14236""14236""14236""20541""20541""20541""20541""22436""22436""69239""69239""69239""69239""69239""78376""240028""240028""240028""240028""67543""67543""239985""239985""239985""102635567""102635567""67374""67374""67374""106143""106143""106143""106143""56277""56277""224171""224171""224171""209294""20357""20357""20357""20357""69053""69053""69053""102640415""102640415""102640415""223754""223754""223754""223754""223754""67731""110082""110082""110082""110082""68070""68070""68070""68070""328479""12224""67516""67516""67516""67516""67516""218975""218975""218975""218975""19214""12289""80795""80795""80795""80795""100042415""100042415""100042415""100042415""18300""18300""18300""109700""110596""110596""110596""110596""328314""328314""328314""328314""328314""328314""328314""328314""192657""192657""192657""192657""192657""19210""19210""19210""19210""14121""14121""14121""14121""14121""74325""74325""74325""66895""66895""20379""20379""20191""20191""20191""20191""20191""20191""20191""20191""94191""94191""320910""320910""73046""73046""73046""73046""73046""16981""16981""14009""14009""14009""14009""14009""18109""18109""18109""18109""18109""319871""319871""319871""319871""11818""11818""20926""20926""20926""67390""67390""67390""237847""73139""73139""73139""73139""194908""194908""70626""70626""70626""209586""209586""625068""625068""16404""16404""16404""15364""15364""15364""15364""71321""71321""71321""102465222""14317""14317""14317""14317""14317""11994""11994""11994""11994""102632700""102632700""102632700""102632700""216033""216033""216033""74928""74928""74928""74928""100504626""16775""16775""16775""16775""66847""66847""66847""66847""77220""77220""81000""235534""235534""235534""235534""71602""71602""71602""66785""66785""66785""66785""244871""244871""70661""70661""77087""75465""75465""75465""170737""170737""170737""14719""14719""14719""14719""14719""93960""93960""93960""93960""93960""75123""75123""75123""75123""75123""102103""102103""102103""108159""108159""210801""210801""434285""434285""434285""434285""434285""244281""244281""12577""17833""17833""76484""76484""70571""70571""70571""70571""70571""76429""76429""76429""233863""233863""233863""233863""233863""233836""233836""233545""233545""23966""23966""23966""23966""23966""23966""23859""23859""23859""21872""21872""21872""14011""14011""14011""503550""210673""67336""67336""16438""16438""16438""16438""16438""20917""18844""18844""18844""18844""18844""18844""56691""56691""56691""56691""100463512""100463512""100463512""100463512""100463512""100463512""100463512""100463512""21415""21415""21415""232077""232077""232077""56150""56150""14804""14804""232035""232035""232035""232035""68140""68140""68140""243771""15258""15258""15258""74354""74354""74354""20336""20336""17992""17992""17992""17992""17992""17992""17992""17992""212996""231769""231769""330164""330164""69162""69162""231225""231225""22062""22062""22062""22062""22062""22062""22062""22062""242748""242748""242721""242721""21401""21401""29876""29876""29876""29876""67344""67344""67344""75578""21687""21687""21687""21687""21687""67770""19266""19266""19266""19266""19266""56079""56079""76299""76299""76299""76299""76299""75691""75691""102636968""102636968""102636968""14590""14590""14590""14590""71510""71510""71510""71510""71510""242274""242274""20447""20447""57257""19221""19221""19221""74645""74645""74645""74645""74645""140493""140493""12480""12480""97112""97112""97112""97112""97112""100526525""100526525""100526525""100526525""12918""12918""12918""12561""12561""13480""13480""13480""13480""329554""329554""329554""329554""14563""14563""14563""14563""94249""94249""94249""94249""94249""94249""94249""94249""72899""72899""72899""18798""19672""19672""99382""99382""99382""99382""241568""241568""241568""241568""11480""11480""11480""69405""69405""69405""69405""67857""67857""15139""15139""11350""11350""11350""11350""11350""11350""68975""68975""68975""54519""54519""54519""54519""71648""71648""71648""71648""71648""18845""18845""18845""18845""66112""66112""66112""66112""75589""75589""75589""75589""75589""75472""19736""19736""102465178""102465178""63913""63913""63913""63913""16565""16565""100040766""100040766""100040766""100040766""241128""241128""241128""241128""241128""241128""241128""241128""17974""50785""50785"
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by cthangav0

I noticed it works when I change 'ont' argument from BP (biological process) to CC (cellular component), but ideally I'd like to get the BP ontology to work.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by cthangav0
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