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[gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO.
sod at cs.wayne.edu
Fri Oct 5 13:23:41 PDT 2007
I'm just curious. How do you calculate the p-values without knowing the
set of genes these genes are coming from?
Sorin Draghici, Ph.D.
Director of the Bioinformatics Core, Karmanos Cancer Institute
Associate Professor Tel: (313) 577-5484
Dept. of Computer Science Fax: (313) 577-6868
Wayne State University
5143 Cass Ave, Room 431 State Hall,
Detroit, MI, 48202
WWW: http://vortex.cs.wayne.edu/Sorin/ (personal)
WWW: http://vortex.cs.wayne.edu/Projects.html (lab)
Check out my recent book: Data Analysis Tools for Microarrays:
Jaak Vilo wrote:
> Dear Emily,
> Please simply go to http://biit.cs.ut.ee/gprofiler/ , paste in the
> very same list and hit g:Profile! The needed answer and many more
> pops up soon. According to GO this is represents almost the entire
> Notch signalling pathway.
> Not only do you get the enrichment results but also a gene by
> gene detailed yet general overview of what is known about those
> genes (e.g. the evidence codes!). Hoovering long enough over the image,
> you get access to many more features like fetching of all annotations
> for any of those genes/proteins, or fetching all those from your query
> that belonged to certain category. KEGG, Reactome, TRANSFAC regulatory
> motifs, etc come up as another bonus.
> At training you may also benefit a lot from the g:Convert and g:Orth
> links that allow you to convert between ID types, and find orthologs,
> The load we have not really stress-tested yet. But it should be ok.
> Calculation speeds you can test using textual output option. This is
> helpful also in case of slower Internet connection, or extremely large
> queries. Current machine is not specially dedicated server (i.e.
> our group runs other tools and calculations sometimes). It is a rather
> regular 4x2 core AMD server Linux box. When is the course?
> (and please send feedback via the form behind the Contact link)
> Ps. To send a colleague the link to exactly the same calculations, you
> can click on "Static URL". For your query it is
> E Dimmer wrote:
>> I'm looking for a tool to demonstrate during a couple of
>> 'Introduction to GO' talks/tutorials and I would be extremely grateful
>> if some tool developers/users could help me choose one.
>> As the audience would be mainly composed of biologists looking at
>> resources that work with UniProt data, I'm looking for an online tool
>> that clusters UniProt protein accessions to display
>> over-representation of GO terms. I need a simple, effective tool that:
>> 1. is freely available
>> 2. can accept human UniProt Accession numbers as input (e.g. Q9Y5Q8)
>> 3. can temporarily cope with the load of ~ 40 people accessing the
>> tool simultaneously (if the tool can alternatively be locally
>> installed, thats fine too)
>> 4. provides a simple interface and outputs a graphic showing showing
>> clustering of proteins around a GO node (if the tool can do more
>> that's fine, but for the limited time-span of the tutorials I need
>> users to easily understand the main idea of the tool and have results
>> returned quickly)
>> 5. finds statistical significance using a multiple-testing correction
>> 6. appreciates the GO DAG, GO evidence codes, and has removed 'NOT'
>> annotations from any imported GO annotations.
>> 7. provides full documentation and is fully supported
>> 8. updates regularly with the GO gene association and OBO files
>> (monthly would be ideal)
>> If you have/use a tool which meets all these requirements, could you
>> please let me know?
>> At the bottom of this e-mail I have listed 55 human UniProt Accessions
>> which all have an annotation to the GO term 'Notch signaling pathway'
>> (GO:0007219) or one of its children, an example of one of the dataset
>> I might supply for the demo.
>> If I find more than one tool that meets the above requirements, I will
>> at least advertise them all, even if I can not demo each of them.
>> Thanks very much,
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