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Gene Ontology Tool Selection

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
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updated by Biostar Biostar • written by Jianguo Lu Jianguo Lu

3 answers

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

• 2 views • link
updated by Ram Ram • written by Qdjm Qdjm

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

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written by Antonio R. Franco Antonio R. Franco

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

• 1 views • link
written by Vitis Vitis

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

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written by jin • jin

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