Question: Open-source tools for GO enrichment in non-model organisms
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gravatar for biotech
3.5 years ago by
biotech540
United States
biotech540 wrote:

I've used Blast2GO in the past but now I'm thinking about switching to open-source tools.

My current idea is get the GO terms database via InterPro and then perform the enrichment with R, possibly topGO. However, my experience with topGO in the past in not the best, compared to Blast2GO. I was missing quite a lot of significant GO terms!

The species is a non-model fungus.

Maybe guys you have a better alternative for my purpose, at least for the enrichment step. Thanks!

R go topgo enrichment • 2.2k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by biotech540
2

You should try goaTools. Is command line based and is quite flexible. For non-model organisms you have to rely on annotation transferred from other organisms which is largely incomplete and could be inaccurate.

ADD REPLYlink written 3.5 years ago by Fidel1.9k

I don't know what blast2go does for mapping terms to genes and for enrichment analysis but it's easy for another approach to produce different results. In particular there are different ways people do enrichment analysis and some may produce a lot of "significant" terms that are not relevant.

My approach would be to transfer annotation by orthology, i.e. build a phylogenetic tree for each gene family in relevant fungal species, including annotated ones. For the enrichment step, any software that can accept custom annotation file (i.e. not tied to existing databases) would do. For my part, I use the approach described in this paper.

ADD REPLYlink written 3.5 years ago by Jean-Karim Heriche21k

It's possible to load annotations to Blast2GO and use their enrichment tool http://course.blast2go.com/b2g_course_li_enrich

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by biotech540

Have you tried https://charite.github.io/software-ontologizer.html

ADD REPLYlink written 3.5 years ago by Khader Shameer18k
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