I have been using clusterProfiler for GO analysis, and I only need to enter the gene ID to get the result. But now I need to analyze some gene that is not annotated, and I get the predicted GO function as follows:
A GO:0008150 0.975 bp biological_process A GO:0009987 0.869 bp cellular process A GO:0051234 0.862 bp establishment of localization B GO:0051179 0.862 bp localization
I would like to know what method can be used to directly perform enrichment analysis on GO ID instead of using gene ID?
•
written
by
LeeLee •
1 answer
Enrichment works because each gene product is annotated with multiple GO terms.
Gene A --> GO1, GO2, GO3
Gene B --> GO1, GO5, GO6
In the toy example, we can see an "enrichment" for GO term GO1, since both genes are annotated with it.
Is unclear what you mean by directly performing enrichment on GO ID alone.
Log in to answer this question.
-
calculating p-value for GO terms
written by azadeh.taati •
-
Gene ontology results differ from cite to software?
written by Merv •
-
How ensembl assigns parent GO terms and its consequence on GO analysis
written by dariober
-
How to do go enrichment under a parent GO term and its child GO term
written by Scabbards •
-
eggNOG v5 annotation file
written by Mehmet
-
How to get genes list from goana function in R
written by smrutimayipanda •
-
TopGO results inconclusive
written by zebratown •
-
FDR values in clusterProfiler
written by karlaarz •
-
topGO is performing enrichment test on GO terms that are not present in my dataset
written by Fabio Marroni
-
levels in gene ontology
written by ashish
