TopGO: Select significant terms under a parent GO term
After running signifance tests on my GOdata, I want to select all the significant GO terms under a parent GO term, which is not significant.
If the parent term is GO:0008152, I want to select all significant child GO terms such as GO:0006521
• 3,956 views
•
link
updated
by
Biostar
•
written
by
QVINTVS_FABIVS_MAXIMVS
•
written
by
QVINTVS_FABIVS_MAXIMVS
1 answer
Method
- install 'ONTO-PERL' module:
- follow README file
- download 'OBO' file -> http://www.geneontology.org/GO.downloads.ontology.shtml
Example: run 'ONTO-PERL' script to get all descendants of GO term 'membrane' GO:0016020
get_descendent_terms.pl gene_ontology_ext.obo GO:0016020 | wc -l 802
get_descendent_terms.pl gene_ontology_ext.obo GO:0016020 > GO0016020.txt
Refrences:
Log in to answer this question.
More posts like this
-
selection of Gene Ontology terms manually
written by harish •
-
How to do go enrichment under a parent GO term and its child GO term
written by Scabbards •
-
How do I get a list of all the GO terms (including children of children etc.) of a parent GO term
written by lekenyon •
-
GO slimming to specific parent term
written by jmah •
-
Do the gene sets of parent terms contains the gene sets of child terms in go ontology?
written by xidianbill •
-
GO Analysis Clarification using GOstats using hyperGTest()
written by brismiller •
-
PANTHER gene ontology - is the bonferroni correction important?
written by sbrown669 •
-
topGO: GO terms but no P-value score
written by khhgng
-
Download gene list associated with GO terms from DAVID
written by qwzhang0601
-
Information Content (IC) of GO terms
written by int11ap1
