Recommend soft for GO enrichment & results visualization

[SOLiDance]

Hi~everyone
I'm doing some transcriptome work,already have a bunch of transcript ID and corresponding GO IDs.
Now I need statistical information for GO categories and want to visualized some results for my paper. But these genes came from a rare species,most GO soft only support several limited species;and to make it worse, the ID list was too long for most web-based GO tools.
I already tried: DAVID,BiNGO,REViGO,GiTools,some Cytoscape plugins,et al.All Failed because of reasons above. Then ran blast2go, it will take such a long time for mapping.Although I got GO IDs,but b2g don't take them as input,only take blast results...Faint!
Could anybody give me a clue? Soft/package to take genes name/GO_IDs as input, and export some visualized results(even do categories count will be accepted) will be fine!
Thank you! and I'am glad to share any information with you~

[turnersd]

GOrilla is good. Paste in a list of genes (or two lists) and get back overrepresented terms and a clickable DAG, color coded by significance. It also allows export to REViGO but I still don't see the utility of REViGO for understanding biology.

[SOLiDance]

GOrilla is good. Paste in a list of genes (or two lists) and get back overrepresented terms and a clickable DAG, color coded by significance. It also allows export to REViGO but I still don't see the utility of REViGO for understanding biology.

Are you sure about this?
I'm sorry,but I just took a look at this website. The first step of Gorilla is to choose organism from 8 provided ones, of course mine is not there yet~
and also it's web-based~
Or maybe could you show me how to modify the workflow to work for me ? thank you!

[chadn737]

What is your organism?

[SOLiDance]

some kind of fish,similar to pufferfish(fugu)

[chadn737]

So do you even have an annotated genome?

Its also unclear to me what your specific goal is here. Are you doing a denovo transcriptome and simply trying to discover whats there? Are you doing differential expression and now want to find enrichment in your differentially expressed genes? Clarify the specific endgoals and that will aid in finding the right tool.

[maubp]

... Then ran blast2go, it will take such a long time for mapping.Although I got GO IDs,but b2g don't take them as input,only take blast results...Faint!

Do you have access to a computer cluster? There are two steps to running Blast2GO, first BLAST which can be done on a cluster and is easy to parallelise, second mapping BLAST matches to GO terms done via database lookups. That can be sped up a lot by installing a local Blast2GO database instead of querying the public database in Spain. This is quite complicated though. We've been looking at Blast2GO via Galaxy as one option - see my Blast2GO for pipelines (b2g4pipe) in the Galaxy Tool Shed entry for details.

Note Blast2GO are offering some sort of premium service for a price nowadays.

[SOLiDance]

No,don't have annotated genome.But we believed it's genome was quite similar with Takifugu rubripes(puffer).
And,these transcripts are differentially expressed ones which I found after diff_exp check step.

[SOLiDance]

Do you have access to a computer cluster? There are two steps to running Blast2GO, first BLAST which can be done on a cluster and is easy to parallelise, second mapping BLAST matches to GO terms done via database lookups. That can be sped up a lot by installing a local Blast2GO database instead of querying the public database in Spain. This is quite complicated though. We've been looking at Blast2GO via Galaxy as one option - see my Blast2GO for pipelines (b2g4pipe) in the Galaxy Tool Shed entry for details.

Note Blast2GO are offering some sort of premium service for a price nowadays.

Thank u~ yeah,I though blast+ won't need much compute resource,so ran on A 4-threads i5 cpu+8G RAM. Fortunately,I do have account to a cluster. Thanks for your help ~