111af33461ddecbdc01107656c60cef12170534a jnavarr5 Wed Jan 8 15:11:57 2020 -0800 Updating redirected links for mm9 found by the uiLinks cronjob. diff --git src/hg/makeDb/trackDb/mouse/ikmc.html src/hg/makeDb/trackDb/mouse/ikmc.html index 633522b..6e7cd0b 100644 --- src/hg/makeDb/trackDb/mouse/ikmc.html +++ src/hg/makeDb/trackDb/mouse/ikmc.html @@ -1,123 +1,123 @@ <H3>Description</H3> <P> This track shows genes targeted by <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/about" TARGET=_BLANK>International Knockout Mouse Consortium (IKMC)</A>, a collaboration to generate a public resource of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome. Gene targets are color-coded by status: <UL> <LI><span style="color: #00F000; font-weight: bold;">Green</span>: Reagent(s) Available</LI> <LI><span style="color: #FFD000; font-weight: bold;">Yellow</span>: In Progress</LI> <LI><span style="color: #0000C8; font-weight: bold;">Blue</span>: Not Started/On Hold</LI> <LI><span style="color: #000; font-weight: bold;">Black</span>: Withdrawn/Problematic</LI> </UL> </P> <P> The <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/aboutkompdcc" TARGET=_BLANK>KnockOut Mouse Project Data Coordination Center (KOMP DCC)</A> is the central database resource for coordinating mouse gene targeting within IKMC and provides web-based query and display tools for IKMC data. In addition, the KOMP DCC website provides a tool for the scientific community to nominate genes of interest to be knocked out by the KOMP initiative.</P> <P> IKMC members include <UL> <LI><a href="https://www.mousephenotype.org/martsearch_ikmc_project/aboutkomp" TARGET=_BLANK>KnockOut Mouse Project (KOMP)</a>, a trans-NIH initiative (USA)</LI> -<LI><a href="http://www.mousephenotype.org/about-ikmc/eucomm" TARGET=_BLANK>European +<LI><a href="https://www.mousephenotype.org/about-impc/about-ikmc/eucomm/" TARGET=_BLANK>European Conditional Mouse Mutagenesis Program (EUCOMM)</a>, funded by the European Union Framework 6 programme (EU)</LI> <LI><a href="http://norcomm.org/index.htm" TARGET=_BLANK>North American Conditional Mouse Mutagenesis Project (NorCOMM)</a>, a Genome Prairie Project (Canada)</LI> <LI><a href="https://www.tigm.org/" TARGET=_BLANK>Texas A&M Institute for Genomic Medicine (TIGM)</a> (USA)</LI> </UL> KOMP includes two production centers: CSD, a collaborative team at the <A HREF="http://www.chori.org/" TARGET=_BLANK>Children's Hospital Oakland Research Institute (CHORI)</A>, the <A HREF="https://www.sanger.ac.uk/research/projects/genetrap/" TARGET=_BLANK>Wellcome Trust Sanger Institute</A> and the University of California at Davis <A HREF="https://www.vetmed.ucdavis.edu/" TARGET=_BLANK>School of Veterinary Medicine</A>, and a team at the <A HREF="https://www.regeneron.com/technology" TARGET=_BLANK>VelociGene</A> division of Regeneron Pharmaceuticals, Inc. -EUCOMM includes <A HREF="http://www.mousephenotype.org/about-ikmc/eucomm" +EUCOMM includes <A HREF="https://www.mousephenotype.org/about-impc/about-ikmc/eucomm/" TARGET=_BLANK>9 participating institutions</A>. NorCOMM includes several <A HREF="http://norcomm.org/research_partners.htm" TARGET=_BLANK>participating institutions</A>. </P> <P> Items displayed as a solid box represent the gene regions targeted by the Regeneron gene knockout strategy. In most cases Regeneron alleles will be complete null alleles that delete the entire protein coding sequence of the target gene.</P> <P> Items displayed as lines connecting short boxes represent the targeting vector construct strategy used by EuCOMM, NorCOMM, and CSD. This strategy relies on the identification of a "critical" exon common to all transcript variants that, when deleted, creates a frame-shift mutation. The short boxes in the middle of an item show the vector features that surround the critical exon. </P> <H3>Methods</H3> <P> Using <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/aboutkompstrategies" TARGET=_BLANK>complementary targeting strategies</A>, the IKMC centers design and create targeting vectors, mutant ES cell lines and, to some extent, mutant mice, embryos or sperm. Materials are distributed to the research community.</P> <P> The <A HREF="https://www.komp.org/index.php?link=5" TARGET=_BLANK>KOMP Repository</A> archives, maintains, and distributes IKMC products. Researchers can order products and get product information from the Repository. Researchers can also express interest in products that are still in the pipeline. They will then receive email notification as soon as KOMP generated products are available for distribution.</P> <P> The process for ordering EUCOMM materials can be found <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/about/eucomm" TARGET=_BLANK>here</A>.</P> <P> The process for ordering TIGM materials can be found <A HREF="https://www.tigm.org/repository/" TARGET=_BLANK>here</A>.</P> <P> Information on NorCOMM products and services can be found <A HREF="http://norcomm.org/accessing_services.htm" TARGET=_BLANK>here</A>.</P> <H3>Credits</H3> <P> Thanks to the <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/about" TARGET=_BLANK>International Knockout Mouse Consortium</A>, and Carol Bult in particular, for providing these data.</P> <H3>References</H3> <p> Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig JT <em>et al</em>. <a href="https://www.nature.com/articles/ng0904-921" target="_blank"> The knockout mouse project</a>. <em>Nat Genet</em>. 2004 Sep;36(9):921-4. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15340423" target="_blank">15340423</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716027/" target="_blank">PMC2716027</a> </p> <p> Collins FS, Finnell RH, Rossant J, Wurst W. <a href="https://www.sciencedirect.com/science/article/pii/S0092867407004643" target="_blank"> A new partner for the international knockout mouse consortium</a>. <em>Cell</em>. 2007 Apr 20;129(2):235. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17448981" target="_blank">17448981</a> </p> <p> International Mouse Knockout Consortium, Collins FS, Rossant J, Wurst W. <a href="https://www.sciencedirect.com/science/article/pii/S0092867406016126" target="_blank"> A mouse for all reasons</a>. <em>Cell</em>. 2007 Jan 12;128(1):9-13. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17218247" target="_blank">17218247</a> </p>