From vanauken at caltech.edu  Tue Aug 21 13:00:08 2007
From: vanauken at caltech.edu (Kimberly Van Auken)
Date: Tue, 21 Aug 2007 13:00:08 -0700
Subject: [gofriends] Re: Fwd: Tools to Visualize/Display GO Terms 
In-Reply-To: <ba8d40550708211235h7be8a116l1447643cb1b3d013@mail.gmail.com>
References: <200708211831.l7LIVQ8Y010966@fafner.Stanford.EDU> <ba8d40550708211235h7be8a116l1447643cb1b3d013@mail.gmail.com>
Message-ID: <46CB4448.5010509@caltech.edu>

Dear Dr. Villeneuve,

Thank you for writing to GO. 

There are a number of publicly available tools for displaying and 
visualizing the results of
your analysis within the context of the GO hierarchy. 

A list of all GO tools, organized according to their use, is maintained 
on the GO's web site:

http://www.geneontology.org/GO.tools.shtml?all

Those tools specifically designed for expression/microarray analysis are 
listed here:

http://www.geneontology.org/GO.tools.shtml?all#micro


I have also forwarded your email to the GO Friends mailing list, as 
members of this list may be
able to help you evaluate which tool is best suited to your needs.

If you aren't on the GO Friends mailing list and would like to sign up, 
here is a link to information
on the consortium's mailing lists:

http://www.geneontology.org/GO.mailing.lists.shtml?all


Best,
Kimberly Van Auken
Database Curator, WormBase

http://www.wormbase.org
http://www.geneontology.org


> From: Villeneuve.Dan at epamail.epa.gov 
> <mailto:Villeneuve.Dan at epamail.epa.gov>
> Date: Tue, 21 Aug 2007 13:30:32 -0500
>
> Hello,
>
> I have used GeneSpring to analyze a set of zebrafish microarray data.
> As part of this analysis, I generated a list of GO categories/terms that
> were significantly enriched for my list of differentially expressed
> genes.  I am looking for a way to display the list in a tree-like format
> that shows the hierarchy of the GO categories on the list.  I tried
> submitting the list using the Advanced Search option but this doesn't
> show the tree-like structure.  Is there a way to accomplish this using
> AmiGO website, or do you know of other publicly available software that
> could be used?
>
> Any assistance you could provide would be appreciated.
>
> ___________________________________
> Dan Villeneuve, Ph.D.
> U.S. EPA  Mid-Continent Ecology Division
> 6201 Congdon Blvd.
> Duluth, MN  55804-2595
> T:  218-529-5217
> F:  218-529-5003
> E-mail:  villeneuve.dan at epa.gov <mailto:villeneuve.dan at epa.gov>
>


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From Mary_Dolan at umit.maine.edu  Tue Aug 21 14:19:10 2007
From: Mary_Dolan at umit.maine.edu (Mary Dolan)
Date: Tue, 21 Aug 2007 17:19:10 -0400
Subject: [gofriends] Re: Fwd: Tools to Visualize/Display GO Terms
In-Reply-To: <46CB4448.5010509@caltech.edu>
References: <200708211831.l7LIVQ8Y010966@fafner.Stanford.EDU>
 <ba8d40550708211235h7be8a116l1447643cb1b3d013@mail.gmail.com>
 <,>
 <46CB4448.5010509@caltech.edu>
Message-ID: <fc.004c4d19322f92ec3b9aca00661c6a9f.322fa134@umit.maine.edu>

Kimberly Van Auken <vanauken at caltech.edu> on Tuesday, August 21, 2007 at 4:00 PM -0500 wrote:
>I have also forwarded your email to the GO Friends mailing list, as 
>members of this list may be
>able to help you evaluate which tool is best suited to your needs.
>
>> From: Villeneuve.Dan at epamail.epa.gov 
>> <mailto:Villeneuve.Dan at epamail.epa.gov>
>> Date: Tue, 21 Aug 2007 13:30:32 -0500
>>
>> Hello,
>>
>> I have used GeneSpring to analyze a set of zebrafish microarray data.
>> As part of this analysis, I generated a list of GO categories/terms that
>> were significantly enriched for my list of differentially expressed
>> genes.  I am looking for a way to display the list in a tree-like format
>> that shows the hierarchy of the GO categories on the list.  I tried
>> submitting the list using the Advanced Search option but this doesn't
>> show the tree-like structure.  Is there a way to accomplish this using
>> AmiGO website, or do you know of other publicly available software that
>> could be used?
>>
>> Any assistance you could provide would be appreciated.
>
>
Dear Dr. Villeneuve,
Here at MGI we have a prototype tool that I think would be of use to you:
http://proto.informatics.jax.org/prototypes/GOTools/web-docs/GO_showselect_ids.html
This returns the GO DAG image with your selected nodes indicated in blue in both png and svg format -- you can also download a .dot file that can be used with GraphViz.

I hope this helps.
Cheers,
Mary

Mary E. Dolan, Ph.D.
************************************
Mouse Genome Informatics Consortium, The Jackson Laboratory
mdolan at informatics.jax.org
(207)288-6439

Research Faculty, NCGIA
Department of Spatial Information Science and Engineering, University of Maine
Boardman Hall 329
University of Maine
Orono, Maine 04469
fax: 207.581.2206
mary_dolan at umit.maine.edu
************************************


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announcements and discussion of the Gene Ontology (GO) project.
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From florian at genomics.princeton.edu  Tue Aug 21 15:08:55 2007
From: florian at genomics.princeton.edu (florian at genomics.princeton.edu)
Date: Tue, 21 Aug 2007 18:08:55 -0400
Subject: [gofriends] Re: Fwd: Tools to Visualize/Display GO Terms
In-Reply-To: <fc.004c4d19322f92ec3b9aca00661c6a9f.322fa134@umit.maine.edu>
References: <200708211831.l7LIVQ8Y010966@fafner.Stanford.EDU>
	<ba8d40550708211235h7be8a116l1447643cb1b3d013@mail.gmail.com> <,>
	<46CB4448.5010509@caltech.edu>
	<fc.004c4d19322f92ec3b9aca00661c6a9f.322fa134@umit.maine.edu>
Message-ID: <20070821180855.24a4jz9a4pwwc00o@gwebmail.princeton.edu>

Hi everybody,

for visualization you might want to check out
http://function.princeton.edu/GOLEM/

"GOLEM: An interactive, graphical gene-ontology visualization, 
navigation,and analysis tool  on the web. GOLEM is a useful tool which 
allows the viewer to navigate and explore a local portion of the Gene 
Ontology (GO) hierarchy. Users can also load annotations for various 
organisms into the ontology in order to search for particular genes, or 
to limit the display to show only GO terms relevant to a particular 
organism, or to quickly search for GO terms enriched in a set of query 
genes."

Additionally (but maybe not that user-friendly) the R-packages GOstats 
and topGO also display their results on the GO graph.

Hope that helps,
Florian

-- 
Florian Markowetz

Princeton University
Lewis-Sigler-Institute, Carl Icahn Lab
Princeton, NJ, 08544

609-258-8236 (lab phone)
609-258-8004 (fax)
florian at genomics.princeton.edu
http://genomics.princeton.edu/~florian


Quoting Mary Dolan <Mary_Dolan at umit.maine.edu>:

> Kimberly Van Auken <vanauken at caltech.edu> on Tuesday, August 21, 2007 
> at 4:00 PM -0500 wrote:
>> I have also forwarded your email to the GO Friends mailing list, as
>> members of this list may be
>> able to help you evaluate which tool is best suited to your needs.
>>
>>> From: Villeneuve.Dan at epamail.epa.gov
>>> <mailto:Villeneuve.Dan at epamail.epa.gov>
>>> Date: Tue, 21 Aug 2007 13:30:32 -0500
>>>
>>> Hello,
>>>
>>> I have used GeneSpring to analyze a set of zebrafish microarray data.
>>> As part of this analysis, I generated a list of GO categories/terms that
>>> were significantly enriched for my list of differentially expressed
>>> genes.  I am looking for a way to display the list in a tree-like format
>>> that shows the hierarchy of the GO categories on the list.  I tried
>>> submitting the list using the Advanced Search option but this doesn't
>>> show the tree-like structure.  Is there a way to accomplish this using
>>> AmiGO website, or do you know of other publicly available software that
>>> could be used?
>>>
>>> Any assistance you could provide would be appreciated.
>>
>>
> Dear Dr. Villeneuve,
> Here at MGI we have a prototype tool that I think would be of use to you:
> http://proto.informatics.jax.org/prototypes/GOTools/web-docs/GO_showselect_ids.html
> This returns the GO DAG image with your selected nodes indicated in 
> blue in both png and svg format -- you can also download a .dot file 
> that can be used with GraphViz.
>
> I hope this helps.
> Cheers,
> Mary
>
> Mary E. Dolan, Ph.D.
> ************************************
> Mouse Genome Informatics Consortium, The Jackson Laboratory
> mdolan at informatics.jax.org
> (207)288-6439
>
> Research Faculty, NCGIA
> Department of Spatial Information Science and Engineering, University 
> of Maine
> Boardman Hall 329
> University of Maine
> Orono, Maine 04469
> fax: 207.581.2206
> mary_dolan at umit.maine.edu
> ************************************
>
>
> --
> 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/
>





--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
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From sod at cs.wayne.edu  Tue Aug 21 16:15:58 2007
From: sod at cs.wayne.edu (Sorin Draghici)
Date: Tue, 21 Aug 2007 19:15:58 -0400
Subject: [gofriends] Re: Fwd: Tools to Visualize/Display GO Terms
In-Reply-To: <46CB4448.5010509@caltech.edu>
References: <200708211831.l7LIVQ8Y010966@fafner.Stanford.EDU> <ba8d40550708211235h7be8a116l1447643cb1b3d013@mail.gmail.com> <46CB4448.5010509@caltech.edu>
Message-ID: <46CB722E.9040708@cs.wayne.edu>

Dear Dan,

Before you dive into the tens of tools listed on the GO website, you may
want to have a look at this paper:

Purvesh Khatri and Sorin Draghici. Ontological analysis of gene
expression data: current tools, limitations, and open problems.
Bioinformatics, 21(18):3587-95, September 2005.
http://vortex.cs.wayne.edu/papers/Ontological_analysis.pdf

Best 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=



Kimberly Van Auken wrote:
> Dear Dr. Villeneuve,
> 
> Thank you for writing to GO.
> There are a number of publicly available tools for displaying and
> visualizing the results of
> your analysis within the context of the GO hierarchy.
> A list of all GO tools, organized according to their use, is maintained
> on the GO's web site:
> 
> http://www.geneontology.org/GO.tools.shtml?all
> 
> Those tools specifically designed for expression/microarray analysis are
> listed here:
> 
> http://www.geneontology.org/GO.tools.shtml?all#micro
> 
> 
> I have also forwarded your email to the GO Friends mailing list, as
> members of this list may be
> able to help you evaluate which tool is best suited to your needs.
> 
> If you aren't on the GO Friends mailing list and would like to sign up,
> here is a link to information
> on the consortium's mailing lists:
> 
> http://www.geneontology.org/GO.mailing.lists.shtml?all
> 
> 
> Best,
> Kimberly Van Auken
> Database Curator, WormBase
> 
> http://www.wormbase.org
> http://www.geneontology.org
> 
> 
>> From: Villeneuve.Dan at epamail.epa.gov
>> <mailto:Villeneuve.Dan at epamail.epa.gov>
>> Date: Tue, 21 Aug 2007 13:30:32 -0500
>>
>> Hello,
>>
>> I have used GeneSpring to analyze a set of zebrafish microarray data.
>> As part of this analysis, I generated a list of GO categories/terms that
>> were significantly enriched for my list of differentially expressed
>> genes.  I am looking for a way to display the list in a tree-like format
>> that shows the hierarchy of the GO categories on the list.  I tried
>> submitting the list using the Advanced Search option but this doesn't
>> show the tree-like structure.  Is there a way to accomplish this using
>> AmiGO website, or do you know of other publicly available software that
>> could be used?
>>
>> Any assistance you could provide would be appreciated.
>>
>> ___________________________________
>> Dan Villeneuve, Ph.D.
>> U.S. EPA  Mid-Continent Ecology Division
>> 6201 Congdon Blvd.
>> Duluth, MN  55804-2595
>> T:  218-529-5217
>> F:  218-529-5003
>> E-mail:  villeneuve.dan at epa.gov <mailto:villeneuve.dan at epa.gov>
>>
> 
> 
> -- 
> 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/
> 
> 


--
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
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Web:          http://www.geneontology.org/


From pfey at northwestern.edu  Thu Aug 23 12:16:45 2007
From: pfey at northwestern.edu (Petra Fey)
Date: Thu, 23 Aug 2007 14:16:45 -0500
Subject: [gofriends] Gene Ontology Newsletter - August issue
Message-ID: <B1C91A96-068D-4B2B-8788-5002F091AF4D@northwestern.edu>

Gene Ontology Newsletter
August 2007, Issue No. 6

In this issue:

1. GO Transporter Terms Improved
2. Gene of the Quarter: CLN3
3. Immunology Wiki
4. New AmiGO SQL web interface
5. Upcoming Meetings

The text of the newsletter can be viewed online or downloaded:

HTML: http://www.geneontology.org/newsletter/current-newsletter.shtml
PDF: http://www.geneontology.org/newsletter/current-newsletter.pdf

Please contact the Gene Ontology Consortium with any comments or
suggestions at gohelp at geneontology.org. Frequently asked questions
may appear as tutorials or tips in upcoming newsletters.

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From camon at ebi.ac.uk  Mon Aug 27 01:40:35 2007
From: camon at ebi.ac.uk (camon at ebi.ac.uk)
Date: Mon, 27 Aug 2007 09:40:35 +0100 (BST)
Subject: [gofriends] 
Message-ID: <52825.81.158.97.69.1188204035.squirrel@webmail.ebi.ac.uk>

GOA releases: August 2007
=======================

GOA (GO Annotation at EBI) is a project run by the European Bioinformatics
Institute that aims to provide assignments of gene products to the Gene
Ontology (GO) resource.

The data can be obtained via:

           EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

           EBI SRS: http://srs.ebi.ac.uk. Search GOA data library

           GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/ ` 
   (updated over the weekend)

           GO CVS: http://www.geneontology.org/GO.CVS.help.html

For further information read: http://www.ebi.ac.uk/GOA or contact
goa at ebi.ac.uk.

Note: In this months release IEA assignments based on Swiss-Prot keyword
assignments have increased due to more manual mappings, while mappings to
Enzyme Commission numbers has dropped. The latter decrease is under
investigation and may be related to a forthcoming EC number format change
at UniProtKB. Partial EC numbers where dashes replace part of the complete
EC number (e.g. EC 3.4.24.-) are currently used for 2 different cases:
- when the catalytic activity of the protein is not known exactly
- when the protein catalyzes a reaction that is known but not yet included
in the IUBMB EC list. To distinguish between these two meanings, UniProtKB
will soon start to use the letter 'n' instead of a dash for the latter
case.

Regards

The UniProt GOA Team


--
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
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From camon at ebi.ac.uk  Mon Aug 27 01:42:22 2007
From: camon at ebi.ac.uk (camon at ebi.ac.uk)
Date: Mon, 27 Aug 2007 09:42:22 +0100 (BST)
Subject: [gofriends] GO Annotation Releases : August 2007
In-Reply-To: <52825.81.158.97.69.1188204035.squirrel@webmail.ebi.ac.uk>
References: <52825.81.158.97.69.1188204035.squirrel@webmail.ebi.ac.uk>
Message-ID: <55751.81.158.97.69.1188204142.squirrel@webmail.ebi.ac.uk>

> GOA releases: August 2007
> =======================
>
> GOA (GO Annotation at EBI) is a project run by the European Bioinformatics
> Institute that aims to provide assignments of gene products to the Gene
> Ontology (GO) resource.
>
> The data can be obtained via:
>
>            EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/
>
>            EBI SRS: http://srs.ebi.ac.uk. Search GOA data library
>
>            GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/ `
>    (updated over the weekend)
>
>            GO CVS: http://www.geneontology.org/GO.CVS.help.html
>
> For further information read: http://www.ebi.ac.uk/GOA or contact
> goa at ebi.ac.uk.
>
> Note: In this months release IEA assignments based on Swiss-Prot keyword
> assignments have increased due to more manual mappings, while mappings to
> Enzyme Commission numbers has dropped. The latter decrease is under
> investigation and may be related to a forthcoming EC number format change
> at UniProtKB. Partial EC numbers where dashes replace part of the complete
> EC number (e.g. EC 3.4.24.-) are currently used for 2 different cases:
> - when the catalytic activity of the protein is not known exactly
> - when the protein catalyzes a reaction that is known but not yet included
> in the IUBMB EC list. To distinguish between these two meanings, UniProtKB
> will soon start to use the letter 'n' instead of a dash for the latter
> case.
>
> Regards
>
> The UniProt GOA Team
>



--
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
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