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

Peter Robinson peter.robinson at
Fri Oct 5 11:40:37 PDT 2007

Hi Emily,

you might want to take a look at the Ontologizer:

it is a Java Webstart application that does most of what you have 
listed. Assuming the local machines have a Java runtime environment as 
well as GraphViz installed, the Ontologizer performs statistical 
analysis with the user's choice of the standard method, the 
topology-based methods described by Alexa et al., as well as our new 
parent-child analysis (the latter two methods cope in different ways 
with some of the dependency problems resulting from the GO DAG 
structure). The Ontologizer implements 6 different multiple-testing 
correction procedures.

I am not entirely sure what you mean by "clusterings of proteins around 
a GO node" (do you mean a graphical representation of all proteins 
annotated to nodes in the graph? That would get to be rather crowded!) 
However, the Ontologizer does list all proteins/genes annotated to any 
node of the graph that is clicked in the graphical representation or 
table, so it is easy to tell which proteins are responsible for 
significantly overrepresented terms.

Users are required to download the OBO files and gene association files. 
While this may be a disadvantage for some, it does mean that everything 
is as up to date as possible and that users can analyze any species for 
which a gene association file is available. Another advantage is that 
affymetrix annotation files can be used directly as gene annotation 
files, which simplifies analysis of affymetrix hybridization results.

Sebastian Bauer in my group has done most of the work above. We would be 
interested in getting your (and others') feedback on these features as 
well as suggestions for new ones.

take care,
Dr. med. Peter N. Robinson, MSc.
Institut für Medizinische Genetik
Universitätsklinikum Charite
Augustenburger Platz 1
13353 Berlin
voice: 49-30-450569124
fax:   49-30-450569915
email: peter.robinson at

> 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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