From erant at psb.ugent.be Tue Oct 2 03:29:19 2007 From: erant at psb.ugent.be (Erick Antezana) Date: Tue, 02 Oct 2007 12:29:19 +0200 Subject: [gofriends] Re: parsing error In-Reply-To: <46EFFE81.9030608@psb.ugent.be> References: <46EFFE81.9030608@psb.ugent.be> Message-ID: <47021D7F.1060103@psb.ugent.be> Dear Midori, once again there is a problem related to the dbxref of the term with id: GO:0009703 : [Term] id: GO:0009703 name: nitrate reductase (NADH) activity namespace: molecular_function def: "Catalysis of the reaction: NO2- (nitrite) + NAD+ + H2O = NO3- (nitrate) + NADH + H+." [EC:1.7.1.1] comment: Note that this function was formerly EC:1.6.6.1. exact_synonym: "assimilatory NADH:nitrate reductase activity" [EC:1.7.1.1] exact_synonym: "NADH-dependent nitrate reductase activity" [EC:1.7.1.1] exact_synonym: "NADH-nitrate reductase activity" [:EC e] exact_synonym: "NADH:nitrate oxidoreductase activity" [EC:1.7.1.1] exact_synonym: "NADH:nitrate reductase" [] exact_synonym: "nitrate reductase (NADH(2)) activity" [EC:1.7.1.1] broad_synonym: "assimilatory nitrate reductase activity" [EC:1.7.1.1] xref_analog: EC:1.7.1.1 xref_analog: MetaCyc:NITRATE-REDUCTASE-(NADH)-RXN is_a: GO:0046857 ! oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor In particular the dbxref of the third listed synonym (exact_synonym: "NADH-nitrate reductase activity" [:EC e]) is wrong. I guess it should be EC:1.7.1.1? Erick Erick Antezana wrote: > Hi, > > I just got the latest GO OBO file. And, while parsing it with the > OBO parser from onto-perl > (http://search.cpan.org/~easr/onto-perl-0.32/) we came across the > following line (61699): > > ATP: protein-L-histidine N-pros-phosphotransferase > > from term: > > [Term] > id: GO:0008256 > name: protein histidine pros-kinase activity > ... > > it is a typo, isn't it? > > cheers, > Erick > -- ================================================================== Erick Antezana http://www.cellcycleontology.org PhD student Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM erant at psb.ugent.be http://www.psb.ugent.be/~erant ================================================================== -- 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/ From midori at ebi.ac.uk Tue Oct 2 04:09:06 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 2 Oct 2007 12:09:06 +0100 (BST) Subject: [gofriends] Re: parsing error In-Reply-To: <47021D7F.1060103@psb.ugent.be> References: <46EFFE81.9030608@psb.ugent.be> <47021D7F.1060103@psb.ugent.be> Message-ID: Dear Erick, Yes, that is another error; thanks again for informing us! I will have a correction committed by the end of the day today. Midori On Tue, 2 Oct 2007, Erick Antezana wrote: > Dear Midori, > > once again there is a problem related to the dbxref of the term with id: > GO:0009703 : > > [Term] > id: GO:0009703 > name: nitrate reductase (NADH) activity > namespace: molecular_function > def: "Catalysis of the reaction: NO2- (nitrite) + NAD+ + H2O = NO3- (nitrate) > + NADH + H+." [EC:1.7.1.1] > comment: Note that this function was formerly EC:1.6.6.1. > exact_synonym: "assimilatory NADH:nitrate reductase activity" [EC:1.7.1.1] > exact_synonym: "NADH-dependent nitrate reductase activity" [EC:1.7.1.1] > exact_synonym: "NADH-nitrate reductase activity" [:EC e] > exact_synonym: "NADH:nitrate oxidoreductase activity" [EC:1.7.1.1] > exact_synonym: "NADH:nitrate reductase" [] > exact_synonym: "nitrate reductase (NADH(2)) activity" [EC:1.7.1.1] > broad_synonym: "assimilatory nitrate reductase activity" [EC:1.7.1.1] > xref_analog: EC:1.7.1.1 > xref_analog: MetaCyc:NITRATE-REDUCTASE-(NADH)-RXN > is_a: GO:0046857 ! oxidoreductase activity, acting on other nitrogenous > compounds as donors, with NAD or NADP as acceptor > > In particular the dbxref of the third listed synonym (exact_synonym: > "NADH-nitrate reductase activity" [:EC e]) is wrong. I guess it should be > EC:1.7.1.1? > > Erick > > Erick Antezana wrote: >> Hi, >> >> I just got the latest GO OBO file. And, while parsing it with the OBO >> parser from onto-perl (http://search.cpan.org/~easr/onto-perl-0.32/) we >> came across the following line (61699): >> >> ATP: protein-L-histidine N-pros-phosphotransferase >> >> from term: >> >> [Term] >> id: GO:0008256 >> name: protein histidine pros-kinase activity >> ... >> >> it is a typo, isn't it? >> >> cheers, >> Erick >> > > -- 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/ From dbarrell at ebi.ac.uk Fri Oct 5 06:55:19 2007 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Fri, 05 Oct 2007 14:55:19 +0100 Subject: [gofriends] EBI MySQL mirror Message-ID: <47064247.4010604@ebi.ac.uk> Hi, The GO MySQL database mirror at mysql.ebi.ac.uk will go down for a few minutes at 16.00 GMT today. This will affect MySQL client connections and GOOSE: http://www.berkeleybop.org/goose Apologies for the short notice. Dan Barrell -- Daniel Barrell EMBL - The EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Phone: +44 (0)1223 492551 Email: dbarrell at ebi.ac.uk -- 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/ From edimmer at ebi.ac.uk Fri Oct 5 10:04:45 2007 From: edimmer at ebi.ac.uk (E Dimmer) Date: Fri, 05 Oct 2007 18:04:45 +0100 Subject: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. Message-ID: <47066EAD.7070703@ebi.ac.uk> 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 -- ************************************ Emily Dimmer GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk ************************************ -- 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/ From jcmatese at genomics.princeton.edu Fri Oct 5 11:25:47 2007 From: jcmatese at genomics.princeton.edu (John Matese) Date: Fri, 5 Oct 2007 14:25:47 -0400 Subject: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. In-Reply-To: <47066EAD.7070703@ebi.ac.uk> References: <47066EAD.7070703@ebi.ac.uk> Message-ID: <07DC4F42-8F79-417F-90FA-DEEF5B767A16@genomics.princeton.edu> Hi Emily, I believe our local implementation of GO-Termfinder fulfills most of your requirements: http://go.princeton.edu/cgi-bin/GOTermFinder Cheers, John Matese On Oct 5, 2007, at 1:04 PM, 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 > > -- > ************************************ > Emily Dimmer > GOA Coordinator > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD, U.K. > Tel: +44 1223 494654 > Fax: +44 1223 494468 > email: edimmer at ebi.ac.uk > ************************************ > > > -- > 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 Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From peter.robinson at t-online.de Fri Oct 5 11:40:37 2007 From: peter.robinson at t-online.de (Peter Robinson) Date: Fri, 05 Oct 2007 20:40:37 +0200 Subject: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. In-Reply-To: <47066EAD.7070703@ebi.ac.uk> References: <47066EAD.7070703@ebi.ac.uk> Message-ID: <47068525.8090904@t-online.de> Hi Emily, you might want to take a look at the Ontologizer: http://www.charite.de/ch/medgen/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, Peter -- Dr. med. Peter N. Robinson, MSc. Institut f?r Medizinische Genetik Universit?tsklinikum Charite Humboldt-Universit?t Augustenburger Platz 1 13353 Berlin Germany voice: 49-30-450569124 fax: 49-30-450569915 email: peter.robinson at charite.de http://www.charite.de/ch/medgen/robinson > 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/ From sod at cs.wayne.edu Fri Oct 5 12:59:16 2007 From: sod at cs.wayne.edu (Sorin Draghici) Date: Fri, 05 Oct 2007 15:59:16 -0400 Subject: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. In-Reply-To: <47066EAD.7070703@ebi.ac.uk> References: <47066EAD.7070703@ebi.ac.uk> Message-ID: <47069794.40304@cs.wayne.edu> Emily, Before going ahead and spend hours trying each of the over 20 tools available in this area, you may want to read a paper reviewing such tools: http://vortex.cs.wayne.edu/papers/Ontological_analysis.pdf Two more points: 1) The statistical significance you desire can only be calculated with respect to some reference set of genes. This is because the p-value represents the probability of obtaining those GO categories if you were to pick random genes from this reference list. So, besides your input, you need to provide such a reference file. For instance, if you used a specific microarray or protein array to monitor the expression levels of these proteins, the list of genes on that array would be the reference list that you need. 2) Secondly, you should be aware that the results of this type of analysis _can_ be influenced (although they shouldn't) by both the type of IDs you use as input, as well as by the source of the annotations. Here is a link to a paper discussing these issues: http://vortex.cs.wayne.edu/papers/Babel.tower.pdf and here is a pointer to a tool, Onto-Translate, that can help you translate between different types of IDs: http://vortex.cs.wayne.edu/ontoexpress/ This work has been supported by several NSF and NIH grants so a (free) registration is required for grant accounting purposes only. 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= 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/ From vilo at quretec.com Fri Oct 5 13:03:50 2007 From: vilo at quretec.com (Jaak Vilo) Date: Fri, 05 Oct 2007 23:03:50 +0300 Subject: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. In-Reply-To: <47066EAD.7070703@ebi.ac.uk> References: <47066EAD.7070703@ebi.ac.uk> Message-ID: <470698A6.6080005@quretec.com> 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/ From sod at cs.wayne.edu Fri Oct 5 13:23:41 2007 From: sod at cs.wayne.edu (Sorin Draghici) Date: Fri, 05 Oct 2007 16:23:41 -0400 Subject: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. In-Reply-To: <470698A6.6080005@quretec.com> References: <47066EAD.7070703@ebi.ac.uk> <470698A6.6080005@quretec.com> Message-ID: <47069D4D.6050308@cs.wayne.edu> 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 >> > > -- > 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 Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From vilo at quretec.com Fri Oct 5 14:01:36 2007 From: vilo at quretec.com (Jaak Vilo) Date: Sat, 06 Oct 2007 00:01:36 +0300 Subject: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. In-Reply-To: <47069D4D.6050308@cs.wayne.edu> References: <47066EAD.7070703@ebi.ac.uk> <470698A6.6080005@quretec.com> <47069D4D.6050308@cs.wayne.edu> Message-ID: <4706A630.2090707@quretec.com> Hi, Sorin Draghici wrote: > I'm just curious. How do you calculate the p-values without knowing the > set of genes these genes are coming from? This is a relevant quetion, of course. Having the whole universe of genes as the background would skew the results towards very broad (and hence somewhat useless) root categories. In this case the background is the set of all genes annotated into the respective broad category. For example, all annotated genes for GO (in given species); all genes known to KEGG; or all genes known to Reactome. Otherwise the comparisons would not be "fair". But indeed, g:Profiler does not support a user-given background set. For example, if one would like to study a strict subset of all transcription regulation related genes, then all broad categories of transcription regulation would be identified. Another useful feature for end-users is that users are allowed to mix any supported ID-s freely in the same query. Genes not known at all (or typos, for example) - would be identified as grey boxes. Unlike white boxes that correspond to known genes that have simply not been annotated to that same category [yet]. Cheers, -Jaak -- 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/ From saurabh at genomeindia.org Fri Oct 5 21:11:57 2007 From: saurabh at genomeindia.org (Saurabh) Date: Sat, 6 Oct 2007 09:41:57 +0530 Subject: [gofriends] EST-to GO Message-ID: <004601c807cf$090d7240$fb01c8c1@dpmb1e7b199633> Hi, I transferred the GO terms to a set of ESTs via similarity to Uniprot entries. I further want to classify/cluster my ESTs (with a graphical output) on the basis of the GO categories. Can anybody suggest a tool for this or should I go ahead a design a script to do that? Rgds Saurabh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20071006/083ca81c/attachment.html From edimmer at ebi.ac.uk Mon Oct 8 06:40:42 2007 From: edimmer at ebi.ac.uk (E Dimmer) Date: Mon, 08 Oct 2007 14:40:42 +0100 Subject: [gofriends] October 2007 GOA release Message-ID: <470A335A.2050807@ebi.ac.uk> GOA releases: October 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. Regards The UniProt GOA Team -- ************************************ Emily Dimmer GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk ************************************ -- 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/ From FMcCarthy at cvm.msstate.edu Mon Oct 8 13:15:57 2007 From: FMcCarthy at cvm.msstate.edu (Fiona McCarthy) Date: Mon, 08 Oct 2007 15:15:57 -0500 Subject: [gofriends] Prokaryote GO Slim set Message-ID: Hi All, Does anyone know of a prokaryote-based GO Slim set that is available for users? thanks, Fiona McCarthy The AgBase Databases Department of Basic Sciences Box 6100 MS 39762-6100 Mississippi State University USA Tel: (+ 1) 662 325 5859 Fax: (+ 1) 662 325 1031 http://www.agbase.msstate.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/ From sgoetz at cipf.es Wed Oct 10 02:43:48 2007 From: sgoetz at cipf.es (Stefan Goetz) Date: Wed, 10 Oct 2007 11:43:48 +0200 Subject: [gofriends] EST-to GO In-Reply-To: <004601c807cf$090d7240$fb01c8c1@dpmb1e7b199633> References: <004601c807cf$090d7240$fb01c8c1@dpmb1e7b199633> Message-ID: <470C9ED4.3030500@cipf.es> Hi Saurabh, you could have a look at www.blast2go.org, a quite user friendly application giving you insights in the functional categories present in your data. You can import your already made annotations (or generate them new with b2g) and generate GO DAG graphs, bar- or pie charts. You will find a tutorial with a short "Quick-start" on how to use B2G on our web page. Best regards, Stefan Goetz Saurabh wrote: > > Hi, > > I transferred the GO terms to a set of ESTs via similarity to Uniprot > entries. I further want to classify/cluster my ESTs (with a graphical > output) on the basis of the GO categories. Can anybody suggest a tool > for this or should I go ahead a design a script to do that? > > > > Rgds > > > > Saurabh > -- -------------------------------------------- Stefan G?tz Bioinformatics Department Centro de Investigaci?n Pr?ncipe Felipe (CIPF) C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanogr?fico) 46013 Valencia, Spain Tel: +34 963289680 Ext. 1011 Fax: +34 963289574 E-Mail: sgoetz at cipf.es http://bioinfo.cipf.es -------------------------------------------- -- 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/ From andreas.schlicker at mpi-inf.mpg.de Thu Oct 11 23:36:00 2007 From: andreas.schlicker at mpi-inf.mpg.de (Andreas Schlicker) Date: Fri, 12 Oct 2007 08:36:00 +0200 Subject: [gofriends] New functional similarity database - FunSimMat Message-ID: <470F15D0.4060001@mpi-inf.mpg.de> Dear all, we just published a paper about our new FunSimMat database (Functional Simlarity Matrix). It provides several precomputed functional similarity measures forall proteins in UniProtKB, and all Pfam and SMART protein families. You can find the paper at http://nar.oxfordjournals.org/cgi/content/abstract/gkm806v1 and FunSimMat at http://funsimmat.bioinf.mpi-inf.mpg.de Here is the abstract: Functional similarity based on Gene Ontology (GO) annotation is used in diverse applications like gene clustering, gene expression data analysis, protein interaction prediction and evaluation. However, there exists no comprehensive resource of functional similarity values although such a database would facilitate the use of functional similarity measures in different applications. Here, we describe FunSimMat (Functional Similarity Matrix, http://funsimmat.bioinf.mpi-inf.mpg.de/), a large new database that provides several different semantic similarity measures for GO terms. It offers various precomputed functional similarity values for proteins contained in UniProtKB and for protein families in Pfam and SMART. The web interface allows users to efficiently perform both semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. All results can be downloaded in tab-delimited files for use with other tools. An additional XML?RPC interface gives automatic online access to FunSimMat for programsand remote services. Kind regards, Andreas -- Andreas Schlicker, M.Sc. Max-Planck-Institute Informatik Department 3: Computational Biology and Applied Algorithmics Campus E1 4 66123 Saarbruecken Germany Phone: +49 681 9325 321 Fax: +49 681 9325 399 Homepage: http://www.mpi-inf.mpg.de/~schlandi -- 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/ From jdopazo at cipf.es Wed Oct 10 03:25:22 2007 From: jdopazo at cipf.es (Joaquin Dopazo) Date: Wed, 10 Oct 2007 12:25:22 +0200 Subject: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. In-Reply-To: <47066EAD.7070703@ebi.ac.uk> References: <47066EAD.7070703@ebi.ac.uk> Message-ID: <066001c80b27$dd43d760$97cb8620$@es> Dear Emily, You can also try FatiGO http://www.fatigo.org, within our functional profiling suite babelomics (http://www.babelomics.org) And you can also find a recent revision on functional profiling tools here: Dopazo, J. (2006) Functional Interpretation of Microarray Experiments. OMICS: A Journal of Integrative Biology. 10:398-410 (find a pdf version following the link: http://bioinfo.cipf.es/docus/papers/publications.html ) Joaquin ------------------------------------------------------- Joaquin Dopazo, PhD Department of Bioinformatics Centro de Investigacion Principe Felipe (CIPF) Av. Autopista del Saler, 16 (Camino de las moreras) 46013 Valencia, Spain Tel.: + 34 96 328 96 80 Fax: + 34 96 328 97 01 http://bioinfo.cipf.es -----Mensaje original----- De: owner-gofriends at genome.stanford.edu [mailto:owner-gofriends at genome.stanford.edu] En nombre de E Dimmer Enviado el: viernes, 05 de octubre de 2007 19:05 Para: go-friends at genome.stanford.edu Asunto: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. 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 -- ************************************ Emily Dimmer GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk ************************************ -- 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 Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From sgoetz at cipf.es Wed Oct 10 03:37:34 2007 From: sgoetz at cipf.es (Stefan Goetz) Date: Wed, 10 Oct 2007 12:37:34 +0200 Subject: [gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO. In-Reply-To: <47066EAD.7070703@ebi.ac.uk> References: <47066EAD.7070703@ebi.ac.uk> Message-ID: <470CAB6E.3040507@cipf.es> Hi Emily. Blast2GO would be a possible option for a GO tool demo as it full fills most of the given criteria and is course/workshop proved. We invite you to test B2G by yourself since it is really easy to start-up and use (if you have Java installed). Just import your list of genes with "import accession list" as ".acc" file and use nearly all the chart and graph options B2G offers. If you need any further support, information or material please do not hesitate in contacting us. Best regards, Stefan Goetz 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 > -- -------------------------------------------- Stefan G?tz Bioinformatics Department Centro de Investigaci?n Pr?ncipe Felipe (CIPF) C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanogr?fico) 46013 Valencia, Spain Tel: +34 963289680 Ext. 1011 Fax: +34 963289574 E-Mail: sgoetz at cipf.es http://bioinfo.cipf.es -------------------------------------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: b2g2.png Type: image/png Size: 150498 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/gofriends/attachments/20071010/bbc130a4/attachment.png From erant at psb.ugent.be Thu Oct 25 07:34:33 2007 From: erant at psb.ugent.be (Erick Antezana) Date: Thu, 25 Oct 2007 16:34:33 +0200 Subject: [gofriends] Re: parsing error In-Reply-To: References: <46EFFE81.9030608@psb.ugent.be> <47021D7F.1060103@psb.ugent.be> Message-ID: Dear Midori, the latest GO file has parsing error in line: 41325 it actually corresponds to a date: Wednesday, 24 October 2007 9: 31:13 am cheers, Erick On Oct 2, 2007, at 1:09 PM, Midori Harris wrote: > Dear Erick, > > Yes, that is another error; thanks again for informing us! I will have > a correction committed by the end of the day today. > > Midori > > On Tue, 2 Oct 2007, Erick Antezana wrote: > >> Dear Midori, >> >> once again there is a problem related to the dbxref of the term >> with id: GO:0009703 : >> >> [Term] >> id: GO:0009703 >> name: nitrate reductase (NADH) activity >> namespace: molecular_function >> def: "Catalysis of the reaction: NO2- (nitrite) + NAD+ + H2O = NO3- >> (nitrate) + NADH + H+." [EC:1.7.1.1] >> comment: Note that this function was formerly EC:1.6.6.1. >> exact_synonym: "assimilatory NADH:nitrate reductase activity" >> [EC:1.7.1.1] >> exact_synonym: "NADH-dependent nitrate reductase activity" >> [EC:1.7.1.1] >> exact_synonym: "NADH-nitrate reductase activity" [:EC e] >> exact_synonym: "NADH:nitrate oxidoreductase activity" [EC:1.7.1.1] >> exact_synonym: "NADH:nitrate reductase" [] >> exact_synonym: "nitrate reductase (NADH(2)) activity" [EC:1.7.1.1] >> broad_synonym: "assimilatory nitrate reductase activity" [EC:1.7.1.1] >> xref_analog: EC:1.7.1.1 >> xref_analog: MetaCyc:NITRATE-REDUCTASE-(NADH)-RXN >> is_a: GO:0046857 ! oxidoreductase activity, acting on other >> nitrogenous compounds as donors, with NAD or NADP as acceptor >> >> In particular the dbxref of the third listed synonym (exact_synonym: >> "NADH-nitrate reductase activity" [:EC e]) is wrong. I guess it >> should be EC:1.7.1.1? >> >> Erick >> >> Erick Antezana wrote: >>> Hi, >>> >>> I just got the latest GO OBO file. And, while parsing it with the >>> OBO parser from onto-perl >>> (http://search.cpan.org/~easr/onto-perl-0.32/) we came across the >>> following line (61699): >>> ATP: protein-L-histidine N-pros-phosphotransferase >>> from term: >>> [Term] >>> id: GO:0008256 >>> name: protein histidine pros-kinase activity >>> ... >>> it is a typo, isn't it? >>> cheers, >>> Erick >> >> >> -- ============================================== Erick Antezana http://www.cellcycleontology.org PhD Student Tel:32 (0)9 3313824 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM erant at psb.ugent.be http://www.psb.ugent.be ============================================== -- 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/ From jdeegan at ebi.ac.uk Tue Oct 30 04:27:27 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 30 Oct 2007 11:27:27 +0000 Subject: [gofriends] Cardiovascular physiology and muscle terms in GO Message-ID: <4727151F.6080308@ebi.ac.uk> Dear GO-Friends, The improvements made at the muscle content meeting (headed by Erika Feltrin, and hosted at CRIBI) and the cardiovascular physiology content meeting (headed by David Hill and hosted at RGD) have now been committed to the GO repository. They will be available for download shortly: http://www.geneontology.org/GO.downloads.ontology.shtml The edits are summarized below. If you would like to comment on the changes made, then please do so via the curator request tracker linked from http://www.geneontology.org/. All comments and contributions are very welcome. Best wishes, Jennifer Deegan GO Curator (On behalf of the Muscle Working Group and the Cardiovascular Physiology Working Group.) Here are the total numbers of changes: Terms: 277 new terms were made. 2 term merges took place. 50 names were changed. 2 general dbxrefs were added. Relationships: 128 new part_of relationships were made. 402 new is_a relationships were made. 33 part_of relationships were deleted. 67 is_a relationships were deleted. Definitions: 274 definitions were added. 80 definitions were changed. 557 definition dbxrefs were added. 2 definition dbxrefs were deleted. Synonyms: 188 new synonyms were added. 130 syonyms were assigned a scope. 21 synonyms were deleted. The new terms added are: GO:0014701 junctional sarcoplasmic reticulum membrane GO:0014702 free sarcoplasmic reticulum membrane GO:0014703 oscillatory muscle contraction GO:0014704 intercalated disc GO:0014705 C zone GO:0014706 striated muscle development GO:0014707 branchiomeric skeletal muscle development GO:0014708 regulation of somitomeric trunk muscle development GO:0014709 positive regulation of somitomeric trunk muscle development GO:0014710 negative regulation of somitomeric trunk muscle development GO:0014711 regulation of branchiomeric skeletal muscle development GO:0014712 positive regulation of branchiomeric skeletal muscle development GO:0014713 negative regulation of branchiomeric skeletal muscle development GO:0014714 myoblast cell fate commitment in head GO:0014715 myoblast cell fate commitment in trunk GO:0014716 satellite cell asymmetric division involved in skeletal muscle regeneration GO:0014717 regulation of satellite cell activation involved in skeletal muscle regeneration GO:0014718 positive regulation of satellite cell activation involved in skeletal muscle regeneration GO:0014719 satellite cell activation GO:0014720 tonic skeletal muscle contraction GO:0014721 twitch skeletal muscle contraction GO:0014722 regulation of skeletal muscle contraction by calcium ion signaling GO:0014723 regulation of skeletal muscle contraction via modulation of calcium ion sensitivity of myofibril GO:0014724 regulation of twitch skeletal muscle contraction GO:0014725 regulation of extraocular skeletal muscle development GO:0014726 negative regulation of extraocular skeletal muscle development GO:0014727 positive regulation of extraocular skeletal muscle development GO:0014728 regulation of the force of skeletal muscle contraction GO:0014729 regulation of the velocity of shortening of skeletal muscle during contraction GO:0014730 skeletal muscle regeneration at neuromuscular junction GO:0014731 spectrin-associated cytoskeleton GO:0014732 skeletal muscle atrophy GO:0014733 regulation of skeletal muscle adaptation GO:0014734 skeletal muscle hypertrophy GO:0014735 regulation of muscle atrophy GO:0014736 negative regulation of muscle atrophy GO:0014737 positive regulation of muscle atrophy GO:0014738 regulation of muscle hyperplasia GO:0014739 positive regulation of muscle hyperplasia GO:0014740 negative regulation of muscle hyperplasia GO:0014741 negative regulation of muscle hypertrophy GO:0014742 positive regulation of muscle hypertrophy GO:0014743 regulation of muscle hypertrophy GO:0014744 positive regulation of muscle adaptation GO:0014745 negative regulation of muscle adaptation GO:0014746 regulation of tonic skeletal muscle contraction GO:0014747 positive regulation of tonic skeletal muscle contraction GO:0014748 negative regulation of tonic skeletal muscle contraction GO:0014801 longitudinal sarcoplasmic reticulum GO:0014802 terminal cisternae GO:0014803 longitudinal sarcoplasmic reticulum lumen GO:0014804 terminal cisternae lumen GO:0014805 smooth muscle adaptation GO:0014806 smooth muscle hyperplasia GO:0014807 regulation of somitogenesis GO:0014808 release of sequestered calcium ion by sarcoplasmic reticulum into cytosol GO:0014809 regulation of skeletal muscle contraction via regulation of the release of sequestered calcium ion GO:0014810 positive regulation of skeletal muscle contraction via regulation of the release of sequestered calcium ion GO:0014811 negative regulation of skeletal muscle contraction via regulation of the release of sequestered calcium ion GO:0014812 muscle cell migration GO:0014813 satellite cell commitment GO:0014814 axon regeneration at neuromuscular junction GO:0014815 initiation of satellite cell activation by growth factor signalling, involved in skeletal muscle regeneration GO:0014816 satellite cell differentiation GO:0014817 satellite cell fate specification GO:0014818 satellite cell fate determination GO:0014819 regulation of skeletal muscle contraction GO:0014820 tonic smooth muscle contraction GO:0014821 phasic smooth muscle contraction GO:0014822 detection of wounding GO:0014823 response to activity GO:0014824 artery smooth muscle contraction GO:0014825 stomach fundus smooth muscle contraction GO:0014826 vein smooth muscle contraction GO:0014827 intestine smooth muscle contraction GO:0014828 distal stomach smooth muscle contraction GO:0014829 vascular smooth muscle contraction GO:0014830 arteriole smooth muscle contraction GO:0014831 gastro-intestinal system smooth muscle contraction GO:0014832 urinary bladder smooth muscle contraction GO:0014833 satellite cell asymmetric division GO:0014834 satellite cell compartment self-renewal involved in skeletal muscle regeneration GO:0014835 myoblast cell differentiation involved in skeletal muscle regeneration GO:0014836 myoblast cell fate commitment involved in skeletal muscle regeneration GO:0014837 myoblast cell fate determination involved in skeletal muscle regeneration GO:0014838 myoblast cell fate specification involved in skeletal muscle regeneration GO:0014839 myoblast migration involved in skeletal muscle regeneration GO:0014841 satellite cell proliferation GO:0014842 regulation of satellite cell proliferation GO:0014843 growth factor dependent regulation of satellite cell proliferation GO:0014844 myoblast cell proliferation involved in skeletal muscle regeneration GO:0014845 stomach body smooth muscle contraction GO:0014846 esophagus smooth muscle contraction GO:0014847 proximal stomach smooth muscle contraction GO:0014848 urinary tract smooth muscle contraction GO:0014849 ureter smooth muscle contraction GO:0014850 response to muscle activity GO:0014852 regulation of skeletal muscle contraction by neural stimulation via neuromuscular junction GO:0014853 regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction GO:0014854 response to inactivity GO:0014855 striated muscle cell proliferation GO:0014856 skeletal muscle cell proliferation GO:0014857 regulation of skeletal muscle cell proliferation GO:0014858 positive regulation of skeletal muscle cell proliferation GO:0014859 negative regulation of skeletal muscle cell proliferation GO:0014860 neurotransmitter secretion involved in control of skeletal muscle contraction GO:0014861 regulation of skeletal muscle contraction via membrane action potential GO:0014862 regulation of skeletal muscle contraction by chemo-mechanical energy conversion GO:0014863 detection of inactivity GO:0014864 detection of muscle activity GO:0014865 detection of activity GO:0014866 skeletal myofibril assembly GO:0014868 cross bridge cycling involved in regulation of the velocity of shortening in skeletal muscle contraction GO:0014869 detection of muscle inactivity GO:0014870 response to muscle inactivity GO:0014871 cross bridge formation involved in regulation of the velocity of shortening in skeletal muscle contraction GO:0014872 myoblast cell division GO:0014873 response to muscle activity involved in regulation of muscle adaptation GO:0014874 response to stimulus involved in regulation of muscle adaptation GO:0014875 detection of muscle activity involved in regulation of muscle adaptation GO:0014876 response to injury involved in regulation of muscle adaptation GO:0014877 response to muscle inactivity involved in regulation of muscle adaptation GO:0014878 response to electrical stimulus involved in regulation of muscle adaptation GO:0014879 detection of electrical stimulus involved in regulation of muscle adaptation GO:0014880 regulation of muscle filament sliding involved in the regulation of the velocity of shortening in skeletal muscle contraction GO:0014881 regulation of myofibril size GO:0014882 regulation of myofibril number GO:0014883 transition between fast and slow fiber GO:0014884 detection of muscle inactivity involved in regulation of muscle adaptation GO:0014885 detection of injury involved in regulation of muscle adaptation GO:0014886 transition between slow and fast fiber GO:0014887 cardiac muscle adaptation GO:0014888 striated muscle adaptation GO:0014889 muscle atrophy GO:0014890 smooth muscle atrophy GO:0014891 striated muscle atrophy GO:0014893 response to rest involved in regulation of muscle adaptation GO:0014894 response to denervation involved in regulation of muscle adaptation GO:0014895 smooth muscle hypertrophy GO:0014896 muscle hypertrophy GO:0014897 striated muscle hypertrophy GO:0014898 cardiac muscle hypertrophy GO:0014899 cardiac muscle atrophy GO:0014900 muscle hyperplasia GO:0014901 satellite cell activation involved in skeletal muscle regeneration GO:0014902 myotube differentiation GO:0014904 myotube cell development GO:0014905 myoblast fusion involved in skeletal muscle regeneration GO:0014906 myotube cell development involved in skeletal muscle regeneration GO:0014908 myotube differentiation involved in skeletal muscle regeneration GO:0014909 smooth muscle cell migration GO:0014910 regulation of smooth muscle cell migration GO:0014911 positive regulation of smooth muscle cell migration GO:0014912 negative regulation of smooth muscle cell migration GO:0014914 myoblast maturation involved in muscle regeneration GO:0014915 regulation of filament sliding speed involved in regulation of the velocity of shortening in skeletal muscle contraction GO:0014916 regulation of lung blood pressure GO:0003008 system process GO:0003009 skeletal muscle contraction GO:0003010 voluntary skeletal muscle contraction GO:0003011 involuntary skeletal muscle contraction GO:0003012 muscle system process GO:0003013 circulatory system process GO:0003014 renal system process GO:0003015 heart process GO:0003016 respiratory system process GO:0003017 lymph circulation GO:0003018 vascular process in circulatory system GO:0003019 central nervous system control of baroreceptor feedback GO:0003020 detection of reduced oxygen by chemoreceptors GO:0003021 detection of increased carbon dioxide by chemoreceptors GO:0003022 detection of pH by chemoreceptors GO:0003023 baroreceptor detection of increased arterial stretch GO:0003024 baroreceptor detection of decreased arterial stretch GO:0003025 baroreceptor regulation of systemic arterial blood pressure GO:0003026 aortic arch baroreceptor control of systemic arterial blood pressure GO:0003027 carotid body chemoreceptor regulation of systemic arterial blood pressure GO:0003028 aortic body chemoreceptor regulation of systemic arterial blood pressure GO:0003029 detection of hypoxic conditions in blood by carotid body chemoreceptors GO:0003030 detection of hydrogen ion GO:0003031 detection of carbon dioxide GO:0003032 detection of oxygen GO:0003033 detection of hypoxic conditions in blood by aortic body chemoreceptors GO:0003034 detection of increased carbon dioxide by aortic body chemoreceptors GO:0003035 detection of increased carbon dioxide by carotid body chemoreceptors GO:0003036 detection of pH by aortic body chemoreceptors GO:0003037 detection of pH by carotid body chemoreceptors GO:0003038 detection of reduced oxygen by aortic body chemoreceptors GO:0003039 detection of reduced oxygen by carotid body chemoreceptors GO:0003040 excitation of vasomotor center by aortic body chemoreceptor signaling GO:0003041 excitation of vasomotor center by carotid body chemoreceptor signaling GO:0003042 vasoconstriction of artery during carotid body chemoreceptor response to lowering of systemic arterial blood pressure GO:0003043 vasoconstriction of artery during aortic body chemoreceptor response to lowering of systemic arterial blood pressure GO:0003044 regulation of systemic arterial blood pressure mediated by a chemical signal GO:0003045 regulation of systemic arterial blood pressure by physical factors GO:0003046 regulation of systemic arterial blood pressure by stress relaxation GO:0003047 regulation of systemic arterial blood pressure by epinephrine GO:0003048 regulation of systemic arterial blood pressure by norepinephrine GO:0003049 regulation of systemic arterial blood pressure by capillary fluid shift GO:0003050 regulation of systemic arterial blood pressure by atrial natriuretic peptide GO:0003051 angiotensin mediated drinking behavior GO:0003052 circadian regulation of systemic arterial blood pressure GO:0003053 circadian regulation of heart rate GO:0003054 circadian regulation of systemic arterial blood pressure by the suprachiasmatic nucleus GO:0003055 circadian regulation of heart rate by the suprachiasmatic nucleus GO:0003056 regulation of vascular smooth muscle contraction GO:0003057 regulation of the force of heart contraction by chemical signal GO:0003058 hormonal regulation of the force of heart contraction GO:0003059 increased force of heart contraction by epinephrine GO:0003060 decreased force of heart contraction by acetylcholine GO:0003061 increased force of heart contraction by norepinephrine GO:0003062 chemical signal regulation of heart rate GO:0003063 negative regulation of heart rate by acetylcholine GO:0003064 regulation of the rate of heart contraction by hormone GO:0003065 positive regulation of heart rate by epinephrine GO:0003066 positive regulation of heart rate by norepinephrine GO:0003067 circadian regulation of systemic arterial blood pressure by hormone GO:0003068 regulation of systemic arterial blood pressure by acetylcholine GO:0003069 acetylcholine vasodilation involved in regulation of systemic arterial blood pressure GO:0003070 regulation of systemic arterial blood pressure by neurotransmitter GO:0003071 renal regulation of systemic arterial blood pressure GO:0003072 renal regulation of systemic arterial blood pressure by control of peripheral vascular resistence GO:0003073 regulation of systemic arterial blood pressure GO:0003074 regulation of diuresis GO:0003075 renal regulation of systemic arterial blood pressure by vasodilation of the peripheral vascular system GO:0003077 negative regulation of diuresis GO:0003078 regulation of natriuresis GO:0003079 positive regulation of natriuresis GO:0003080 negative regulation of natriuresis GO:0003081 regulation of systemic arterial blood pressure by renin-angiotensin GO:0003082 angiotensin mediated positive regulation of renal output GO:0003083 angiotensin mediated negative regulation of renal output GO:0003084 positive regulation of systemic arterial blood pressure GO:0003085 negative regulation of systemic arterial blood pressure GO:0003086 regulation of systemic arterial blood pressure by local renal renin-angiotensin GO:0003087 increased force of heart contraction by neuronal epinephrine GO:0003088 increased force of heart contraction by circulating epinephrine GO:0003089 increased force of heart contraction by circulating epinephrine-norepinephrine GO:0003090 increased force of heart contraction by neuronal epinephrine-norepinephrine GO:0003091 renal water homeostasis GO:0003092 renal water retention GO:0003093 regulation of glomerular filtration GO:0003094 glomerular filtration GO:0003095 pressure natriuresis GO:0003096 renal sodium ion transport GO:0003097 renal water transport GO:0003098 tubuloglomerular feedback GO:0003099 positive regulation of the force of heart contraction by chemical signal GO:0003100 regulation of systemic arterial blood pressure by endothelin GO:0003101 regulation of systemic arterial blood pressure by circulatory epinephrine-norepinephrine GO:0003102 angiotensin-mediated positive regulation of diuresis GO:0003103 positive regulation of diuresis GO:0003104 positive regulation of glomerular filtration GO:0003105 negative regulation of glomerular filtration GO:0003106 angiotensin-mediated regulation of glomerular filtration GO:0003107 angiotensin-mediated positive regulation of natriuresis GO:0003108 negative regulation of the force of heart contraction by chemical signal GO:0003109 increased force of heart contraction by circulating norepinephrine GO:0003110 increased force of heart contraction by neuronal norepinephrine GO:0003111 positive regulation of heart rate by circulating epinephrine GO:0003112 positive regulation of heart rate by neuronal epinephrine GO:0003113 positive regulation of heart rate by neuronal norepinephrine GO:0003114 positive regulation of heart rate by circulating norepinephrine GO:0003115 regulation of vasoconstriction by epinephrine GO:0003116 regulation of vasoconstriction by norepinephrine GO:0003117 regulation of vasoconstriction by circulating norepinephrine GO:0003118 regulation of vasoconstriction by neuronal norepinephrine GO:0003119 regulation of vasoconstriction by neuronal epinephrine GO:0003120 regulation of vasoconstriction by circulating epinephrine GO:0003121 regulation of vasodilation by epinephrine GO:0003122 regulation of vasodilation by norepinephrine GO:0003123 regulation of vasodilation by circulating epinephrine GO:0003124 regulation of vasodilation by neuronal epinephrine GO:0003125 regulation of vasodilation by circulating norepinephrine GO:0003126 regulation of vasodilation by neuronal norepinephrine GO:0014917 positive regulation of diuresis by pressure natriuresis GO:0014918 positive regulation of natriuresis by pressure natriuresis -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium -- 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/