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[gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO.

Sorin Draghici sod at cs.wayne.edu
Fri Oct 5 13:23:41 PDT 2007


Jaak,

I'm just curious. How do you calculate the p-values without knowing the
set of genes these genes are coming from?

Regards,


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:
http://www.crcpress.com/shopping_cart/products/product_detail.asp?sku=C3154&parent_id=&pc=



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,
> respectively.
> 
> 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?
> 
> Enjoy!
> (and please send feedback via the form behind the Contact link)
> 
> -Jaak
> 
> Ps. To send a colleague the link to exactly the same calculations, you
> can click on "Static URL". For your query it is
> http://biit.cs.ut.ee/gprofiler/index.cgi?organism=hsapiens&query=O00548+O14672+P05067+P25963+P46531+P49768+P49810+P50553+P78504+P78536+Q04721+Q06330+Q0VG99+Q12860+Q12948+Q16873+Q4KMR2+Q59ED8+Q5SPL1+Q5SSY7+Q5STG5+Q5SXM3+Q5VTD0+Q86UW9+Q86Y01+Q86YT6+Q8IZL2+Q8N9I9+Q8NBS4+Q8NFT8+Q8WW43+Q92542+Q92585+Q96AX9+Q96BI3+Q96JK9+Q96T58+Q99466+Q99958+Q9BRJ9+Q9BYE0+Q9H3D4+Q9H488+Q9HD90+Q9NQ87+Q9NR61+Q9NYJ7+Q9NZ42+Q9UBP5+Q9UBV2+Q9UM47+Q9UQ52+Q9Y219+Q9Y2E6+Q9Y5J3&analytical=1&domain_size_type=annotated&term=&significant=1&sort_by_structure=1&user_thr=1.00&output=png
> 
> 
> E Dimmer wrote:
>> Hi,
>>
>> 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,
>>
>> Emily
>>
>> **
>>
>> O00548
>> O14672
>> P05067
>> P25963
>> P46531
>> P49768
>> P49810
>> P50553
>> P78504
>> P78536
>> Q04721
>> Q06330
>> Q0VG99
>> Q12860
>> Q12948
>> Q16873
>> Q4KMR2
>> Q59ED8
>> Q5SPL1
>> Q5SSY7
>> Q5STG5
>> Q5SXM3
>> Q5VTD0
>> Q86UW9
>> Q86Y01
>> Q86YT6
>> Q8IZL2
>> Q8N9I9
>> Q8NBS4
>> Q8NFT8
>> Q8WW43
>> Q92542
>> Q92585
>> Q96AX9
>> Q96BI3
>> Q96JK9
>> Q96T58
>> Q99466
>> Q99958
>> Q9BRJ9
>> Q9BYE0
>> Q9H3D4
>> Q9H488
>> Q9HD90
>> Q9NQ87
>> Q9NR61
>> Q9NYJ7
>> Q9NZ42
>> Q9UBP5
>> Q9UBV2
>> Q9UM47
>> Q9UQ52
>> Q9Y219
>> Q9Y2E6
>> Q9Y5J3
>>
> 
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