Hello EagleEye. Thanks for suggestion! But for custom database/ non-model organisms I've to create GO/KEGG files as explained by you here - A: GO enrichment analysis using a Text file with all the genes and GO ids associat . Again, I've to go to the source such as 'geneontology.org' to get GO entries & their associated Genes.. Is there any way I just give taxid & get associated Geneontology?
GO Annotations from geneontology.org
Hello Biostars!
Can anyone tell me how to get GO Ontology (Molecular function, Cellular Component & Biological process ) along with genes involved in it from GAF (go-annotation-file) or geneontology.org for a particular species?
Right now I'm getting from GAF:
Column Content Required? Cardinality Example
1 DB required 1 UniProtKB
2 DB Object ID required 1 P12345
3 DB Object Symbol required 1 PHO3
4 Qualifier optional 0 or greater NOT
5 GO ID required 1 GO:0003993
6 DB:Reference (|DB:Reference) required 1 or greater SGD_REF:S000047763|PMID:2676709
7 Evidence Code required 1 IMP
8 With (or) From optional 0 or greater GO:0000346
9 Aspect required 1 F
10 DB Object Name optional 0 or 1 Toll-like receptor 4
11 DB Object Synonym (|Synonym) optional 0 or greater hToll|Tollbooth
12 DB Object Type required 1 protein
13 Taxon(|taxon) required 1 or 2 taxon:9606
14 Date required 1 20090118
15 Assigned By required 1 SGD
16 Annotation Extension optional 0 or greater part_of(CL:0000576)
17 Gene Product Form ID optional 0 or 1 UniProtKB:P12345-2
Please help..Thank you. :)
1 answer
You can try GeneSCF,
Example: A: How to look up GO terms associated to a certain organism?
Hi, in 'gene ontology' which closest organism are you looking for ? You can use organism code (3. Preparing database) in GeneSCF to retrieve the terms and genes specific to an organism of interest.
Log in to answer this question.
More posts like this
-
How can I conduct a meta-analysis of RNA-seq or microarray data?
written by wyt1995 •
-
GO enrichment and KEGG output empty
written by estpallag •
-
GO annotations into GFF3
written by Ric
-
Jupyter python cell will not finish to completion how to fix hash(id(seq) issue
written by bcheda •
-
OMA: gene_function.gaf output file empty
written by lassancejm •
-
Parsing ./spoNA.xml file failed, please check the file!
written by Parham
