Question

Gene Ontology Tool Selection

1

Entering edit mode

13.4 years ago

Jianguo Lu ▴ 200

I am trying to do the gene ontology analysis based on the gene duplication to see weather there are any difference between gene duplication genes and control. I used the BLAST2GO a lot to get some difference. However, there is no any difference comparing with control. I think it looks like BLAST2GO try to put every possible GO term together, so it overwhelmed the difference. Is anyone know more aggressive Gene Ontology software for my case? Appreciate it!

gene blast enrichment • 3.9k views

ADD COMMENT • link updated 7.4 years ago by Biostar 20 • written 13.4 years ago by Jianguo Lu ▴ 200

Ram · Answer 1 · 2011-06-14

4

Entering edit mode

13.4 years ago

Qdjm 1.9k

If you are trying to find enriched Gene Ontology terms, DAVID is very popular.

The Gene Ontology website has a section for term enrichment tools, there are about 15 listed there.

You might also find these Biostar topics helpful: 1, 2

ADD COMMENT • link updated 5.2 years ago by Ram 44k • written 13.4 years ago by Qdjm 1.9k

0

Entering edit mode

the section for term enrichment tools has been discontinued...

ADD REPLY • link 7.4 years ago by Antonio R. Franco ★ 5.1k

score 2 · Answer 2 · 2011-07-01

2

Entering edit mode

13.4 years ago

Vitis ★ 2.6k

The GOstat package in R seems to be good to find GO enrichments.

ADD COMMENT • link 13.4 years ago by Vitis ★ 2.6k

score 1 · Answer 3 · 2016-11-04

1

Entering edit mode

8.1 years ago

jin ▴ 80

If you are working on plants, try PlantRegMap which annotated GO annotation for all genes from 165 plant species then do enrichment analysis.

ADD COMMENT • link 8.1 years ago by jin ▴ 80