Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Jaak Vilo vilo at quretec.com
Fri Oct 5 13:03:50 PDT 2007


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
> 

--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list