MGI-News and Announcements from the Mouse Genome Informatics database resource

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for genome features by name, symbol, synonym, homolog, allele, or accession ID:</li> <ul><li>p53 protein cell cycle DNA damage</li><li>Notch1</li><li>NM_053172</li><li>AT3</li></ul><li>Search for genome features and vocabulary terms by keywords or accession ID. 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class="yuimenuitemlabel">Function</a> <div id="navBarFunction" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gene_ontology" onMouseOver="return overlib('Browse the Gene Ontology and mouse annotations in MGI.',ANCHOR, 'navBarFunction', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> GO Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/marker/" onMouseOver="return overlib('Search for genes and genome features by symbol, name, location, gene ontology classification or phenotype.',ANCHOR, 'navBarFunction', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Genes & Markers Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Obtain sets of MGI IDs for use in GO tools.',ANCHOR, 'navBarFunction', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Batch Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/function.shtml">More</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Strains / SNPs</a> <div id="navBarStrains" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/home/strain" onMouseOver="return overlib('Search for strains by name, synonyms, or attributes.',ANCHOR, 'navBarStrains', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();">Strain Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/snp" onMouseOver="return overlib('Search for SNPs by strain(s), SNP attributes, genomic position, or associated genes.',ANCHOR, 'navBarStrains', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> SNP Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgv/" onMouseOver="return overlib('Compare genome features of de novo sequenced mouse strains.',ANCHOR, 'navBarStrains', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Multiple Genome Viewer (MGV)</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/home/strain">More</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a id="navBarHomology" class="yuimenuitemlabel" href="https://www.informatics.jax.org/homology.shtml" onMouseOver="return overlib('Find out more about Homology relationships in MGI.',ANCHOR, 'navBarHomology', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> Homology</a></li>  <li class="yuimenuitem"><a id="navBarMTB" class="yuimenuitemlabel" href="https://tumor.informatics.jax.org/mtbwi/index.do" onMouseOver="return overlib('MTB provides information on the frequency, pathology, and genetics of spontaneous and induced tumors in mice.',ANCHOR, 'navBarMTB', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> Tumors</a></li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Sequence Searches</a> <div id="navBarSequences" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi" onMouseOver="return overlib('Search for sequence similarity using BLAST at NCBI.',ANCHOR, 'navBarSequences', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> BLAST at NCBI</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="http://jbrowse.informatics.jax.org/?data=data/GRCm39" onMouseOver="return overlib('Create a graphical display of genome features from regions of the mouse genome.',ANCHOR, 'navBarSequences', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> JBrowse Genome Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Input a list of gene IDs or symbols and retrieve 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</li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Ontologies</a> <div id="navBarVocabularies" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gene_ontology" onMouseOver="return overlib('Browse the Gene Ontology and mouse annotations in MGI.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> GO Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/disease" onMouseOver="return overlib('Browse for a human disease or condition term to find mouse models.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Human Disease (DO) Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/mp_ontology" onMouseOver="return overlib('Search for a phenotype term to find relevant mutant genotypes.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Mammalian Phenotype (MP) Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16039" onMouseOver="return overlib('Search or browse for anatomical structures; includes links to associated expression results.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Mouse Developmental Anatomy Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gxd/ma_ontology" onMouseOver="return overlib('An extensive ontology of anatomical structures for the postnatal mouse.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Adult Mouse Anatomy Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/hp_ontology" onMouseOver="return overlib('Search for a human phenotype ontology term to find relevant human diseases.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Human Phenotype (HPO) Browser</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a id="navBarBatch" class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Input a list of gene IDs or symbols and retrieve other database IDs and gene attributes (e.g. phenotypes, GO).',ANCHOR, 'navBarBatch', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> Batch Query</a></li> <li class="yuimenuitem"><a id="navBarMine" class="yuimenuitemlabel" href="https://www.mousemine.org" onMouseOver="return overlib('Access MGI data via InterMine.',ANCHOR, 'navBarMine', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> MouseMine</a></li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Mouse Genome Browsers</a> <div id="navBarGenomeBrowsers" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem"><a id="navBarJBrowse" 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These data include the Sanger MGP (v5) SNP set. Use our preeminent <a href="https://www.informatics.jax.org/snp" target="_blank">SNP Query</a> to search for SNPs by gene symbols or chromosomal regions across 101 mouse strains. Search results are limited to 100,000 SNPs (displayed or downloaded), and filters are available to refine search results that exceed the return limit.</dt> <dt>To query this large data set efficiently, we implemented the search with Elasticsearch, which allows large data sets to be queried in parallel and improves search speeds. We plan on using this search for other large data sets in MGI/GXD.</dt> <dt>In order to update the SNP coordinates to GRCm39 we temporarily lost the dbSNP function classes, such as whether the SNP is in an intron or coding region, and therefore, the Function Class filter in a SNP summary report is limited to "within coordinates of." A future release will provide more function classes. The function classes for individual SNPs can be found by searching <a href="https://www.alliancegenome.org" target="_blank">The Alliance of Genome Resources</a> with the RefSNP ID, one ID at a time. For queries that specify one or more Reference strains, MGI's Allele Agreement filters restrict results to SNPs with strain allele calls that agree or differ from reference strain alleles.</dt> <dt><b>New links to GlyGen</b>.</dt> <dt>New to the Protein Information section of Gene Detail pages are links to GlyGen for carbohydrate and glycoconjugate data. For an example, see the <a href="https://www.informatics.jax.org/marker/MGI:97838" target="_blank">Eprs1</a> Gene Detail page.</dt> </dl> </td> </tr> </table> <tr><td><a id="jun1_2024"></a> <table class="outline" width="100%"> <tr><td class="enhance">June 1, 2024</td></tr> <tr><td> <dl class="linkedList"> <dt><b>MGD 1.0 was released on the World Wide Web 30 years ago.</b></dt> <dt>The first release of the Mouse Genome Database was launched on the World Wide Web in June of 1994. This release encompassed several projects initiated at The Jackson Laboratory, including GBASE, the Mouse Locus Catalog (MLC), the Mouse Linkage Database and Programs (MLDP), the Homology Database and Programs (HMDP), and probes and PCR databases describing molecular reagents and polymorphisms (MusProb and MusPCR). MGD 1.0 combined all of these earlier disparate databases into one coherent system, eliminating redundancy and making possible new data integration and analysis. Also included was the Encyclopedia of the Mouse Genome, a suite of software tools for browsing mouse genetic data and displaying genetic and cytogenetic maps. This application was a finalist for a Computerworld Smithsonian Award for Innovation in Information Technology.</dt> <dt>This web page sumarizes each <a href="https://www.informatics.jax.org/mgihome/other/mgicron.shtml" target="_blank"> MGI database release</a>.</dt> <dt><b>A new cookie banner appears at the bottom of MGI web pages.</b></dt> <dt>In order to be compliant with the European Union's new data privacy and security law, the General Data Protection Regulation (GDPR), we offer a cookie banner at the bottom of MGI web pages to manage your cookie preferences.</dt> <dt>MGI uses HTTP cookies, some of which are Essential for basic web operation. You cannot opt out of these cookies.</dt> <dt>Other cookies are used for Analytics, in which the IP address of your browser and each query against the MGI website is logged. This Information is used to generate usage summary statistics for the site and for reporting to funding agencies. The Information is not used to identify individuals or organizations and is not shared with third parties. You may choose to opt out of the Analytics cookies. An opt out selection is retained for 6 months. The default for Analytics cookies is opt in.</dt> </dt> </dl> </td> </tr> </table> <tr><td><a id="feb13_2024"></a> <table class="outline" width="100%"> <tr><td class="enhance">February 13, 2024</td></tr> <tr><td> <dl class="linkedList"> <dt><b>We removed two features from Marker Detail pages:</b></dt> <dt>We deleted the Interactions section with interacting microRNAs and its linked Interaction Explorer. Instead, for a marker's molecular and genetic interactions, follow the Alliance gene page link in the top, Summary section, of Marker Detail pages.</dt> <dt>Also no longer present on Marker Detail pages are the GBrowse thumbnails of the marker region. These were found in the Location & Maps section and linked to JBrowse. The text link ("View this region in JBrowse") remains. </dt> </dt> </dl> </td> </tr> </table> <tr><td><a id="jan22_2024"></a> <table class="outline" width="100%"> <tr><td class="enhance">January 22, 2024</td></tr> <tr><td> <dl class="linkedList"> <dt>A new feature in the MGI SNP query allows you to mouseover a strain to see the number of its SNPs included in MGI.</dt> <dt>The MGI Prototypes are being decommissioned with the exception of VLAD, a tool for visualizing GO annotation enrichment. An upgraded VLAD can be found among the <a href="https://www.informatics.jax.org/mgihome/menus/tools.shtml">Analysis Tools</a>.</dt> <dt>The Human - Mouse Disease Connection (HMDC) phenotype ID search tool allows you to add matching MP and HPO terms to your HMDC searches. This tool has been updated to include more robust lexical matching between the MP and HPO vocabularies. See also the previous update from <a href="https://www.informatics.jax.org/mgihome/news/whatsnew.shtml#sept11_2023">September 11, 2023</a>. </dt> </dt> </dl> </td> </tr> </table> <tr><td><a id="dec11_2023"></a> <table class="outline" width="100%"> <tr><td class="enhance">December 11, 2023</td></tr> <tr><td> <dl class="linkedList"> <dt><b>The Global Biodata Coalition (GBC) designated GXD a Global Core Biodata Resource.</b></dt> <dt><a href="https://globalbiodata.org/what-we-do/global-core-biodata-resources/" target="_blank"><img src="https://www.informatics.jax.org/mgihome/homepages/images/GCBR-LogoSm-RGB.png" alt="GCBR_Logo" width="201" height="85"></img></a></dt> <dt>Global Core Biodata Resources are biodata resources that are of fundamental importance to the wider biological and life sciences community and the long term preservation of biological data. They: <ul> <li>provide free and open access to their data,</li> <li>are used extensively both in terms of the number and distribution of their users,</li> <li>are mature and comprehensive,</li> <li>are considered authoritative in their field,</li> <li>are of high scientific quality, and</li> <li>provide a professional standard of service delivery.</li> </ul> Their operation is based on well-established life-cycle management processes and well-understood dependencies with related data resources. GCBRs have either terms of use or specific licenses that conform to the Open Definition, to enable the reuse of data. </dt> <dt>GXD and MGD, the two main components of MGI, are now both designated as GCBRs. <a href="https://www.informatics.jax.org/mgihome/news/news_2022.shtml#dec15_2022" target="_blank">MGD was already named a GCBR in 2022</a>.</dt> </dl> </td> </tr> </table> <tr><td><a id="sept11_2023"></a> <table class="outline" width="100%"> <tr><td class="enhance">September 11, 2023</td></tr> <tr><td> <dl class="linkedList"> <dt><b>Human - Mouse: Disease Connection search refinements.</b></dt> <dt>The Human Phenotype Ontology (HPO) and Mammalian Phenotype (MP) Ontology are distinct vocabularies that cover similar concepts. With this release, we added a tool to find related terms in the two ontologies, and add these to a Human - Mouse: Disease Connection (<a href="https://www.informatics.jax.org/diseasePortal" target="_blank">HMDC</a>) phenotype ID search. This permits you to find both human and mouse phenotypic results when searching by ID.</dt> <dt>Previously, when you used the Human Phenotype Ontology (<a href="https://www.informatics.jax.org/vocab/hp_ontology" target="_blank">HPO</a>) Browser, and you clicked on the number of annotations, the search forwarded to the HMDC and the search was limited to just human phenotype annotations. With this release, however, use the "Click to modify search" button and you will have the option of finding and adding related mammalian phenotype terms to the HMDC search results. </dt> </dl> </td> </tr> </table> <tr><td><a id="may30_2023"></a> <table class="outline" width="100%"> <tr><td class="enhance">May 30, 2023</td></tr> <tr><td> <dl class="linkedList"> <dt><b>MGI has improved its representation of the pseudoautosomal region (PAR).</b></dt> <dt> <ul> <li>A search for Chr XY with the Genes & Markers Query now returns all PAR markers, placed in the PAR by genome coordinates or by genetic mapping. PAR markers with genome coordinates can still be returned by coordinate searches of the corresponding chromosome (X or Y).</li> <li>MGI now represents sequence-verified PARX / PARY homologous loci as distinct markers, with Chr X / Chr Y genome coordinates, respectively, and gene detail pages provide links to the Homologous PAR Feature. As an example, see the <a href="https://www.informatics.jax.org/marker/MGI:2384747" target="_blank">Erdr1x</a> Gene Detail Page.</li> </ul> </dt> <dt>The Multiple Genome Viewer (MGV) now includes 2 <i>Xenopus</i> genomes: the African clawed frog, <i>X. laevis</i>, and the the Western clawed frog, <i>X. tropicalis</i>. <i>X. laevis</i> is an allotetraploid (2n = 36) of hybrid origin. The resulting <i>X. laevis</i> genome has a set of ancestral 'long' (L) and 'short' (S) chromosomes, with extensive L/S homoeology for genes that have been retained on the S subgenome. The <i>X. laevis.L</i> and <i>X. laevis.S</i> subgenomes are represented as separate genomes in the MGV. </td> </dl> </td> </tr> </table> <tr><td><a id="feb13_2023"></a> <table class="outline" width="100%"> <tr><td class="enhance">February 13, 2023</td></tr> <tr><td> <dl class="linkedList"> <dt><b>QTL Detail Pages now include candidate genes and QTL interactions.</b></dt> <dt>QTL Detail Pages summary section now includes pop-ups for: <ul> <li>Candidate Genes <ul> <li>Potential candidate genes for the featured QTL are shown with their genome locations, details describing their candidacy, supporting references, and links to the candidate genes' detail pages. Reciprocally, pages for QTL candidate genes show details and links to detail pages for QTL the genes are potential candidates for. As an example, see the top, Summary section, of the <a href="https://www.informatics.jax.org/marker/MGI:104787" target="_blank">Skts2 QTL Detail page</a>.</li> </li> </ul></li> <li>QTL Interactions <ul> <li>For interacting QTL, QTL detail pages show interacting QTL, their genetic and genome locations, interaction type (enhancement or suppression), and supporting references. As an example, see the top, Summary section, of the <a href="https://www.informatics.jax.org/marker/MGI:2656547" target="_blank">Lmr14 QTL Detail page</a>.</li> </ul></li> </ul> </dt> <dt>GXD鈥檚 <a href="https://www.informatics.jax.org/gxd/profile">Expression Profile Search</a> now includes the ability to search for genes detected in selected tissues "And Nowhere Else."</dt> </dl> </td> </tr> </table> <tr><td><a id="jan5_2023"></a> <table class="outline" width="100%"> <tr><td class="enhance">January 5, 2023</td></tr> <tr><td> <dl class="linkedList"> <dt><b>MGI is now supporting the more secure HTTPS protocol.</b></dt> <dt>Hypertext Transfer Protocol Secure (HTTPS) adds a Secure Sockets Layer (SSL) to HTTP. This encrypts exchanges between your browser and the MGI web server and reduces the risk of a malicious entity intercepting your web interactions. </dt> <dt>Some web browsers by default are set to only use HTTPS and in order to access MGI, you had to turn off that preference. With this update, you have one less reason to turn that off. </dt> <dt>MouseMine has already been using HTTPS for about a year. The International Mouse Strain Resource (IMSR) and the Mouse Models of Human Cancer Database (MMHCdb) will be using HTTPS in future releases. </dt> </dl> </td> </tr> </table> </td> </tr> </table> </div>  <table style="font-size:12" border=0 width="99%"> <tr> <td colspan="3"><HR noshade="noshade"/ color="#d0e0f0" width="100%"> <center style="font-size:10px;"> <span style="float: left;">Contributing Projects:</span> <br> Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO) </center> </td> </tr> <tr> <td width="33%" style="font-size:9px;"> <A HREF="https://www.informatics.jax.org/mgihome/other/citation.shtml"> Citing These Resources</A> <BR> <A HREF="https://www.informatics.jax.org/mgihome/other/mgi_funding.shtml"> Funding Information</A> <BR> <A HREF="https://www.informatics.jax.org/mgihome/other/copyright.shtml"> Warranty Disclaimer, Privacy Notice, Licensing, & Copyright</A> <BR> Send questions and comments to <A HREF="https://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml"> User Support</A>. </td> <td WIDTH="34%" ALIGN=center style="font-size:9px;"> last database update<BR> 11/19/2024<BR> MGI 6.24 </td> <td WIDTH="33%" ALIGN=right style="font-size:9px;"> <A HREF="https://www.jax.org/" border=0 style="background-color: transparent"> <IMG SRC="https://www.informatics.jax.org/webshare/images/jax_logo_small.png" BORDER=0 ALT="The Jackson Laboratory"></A> </td> </tr> <tr> <td colspan="3"> <HR noshade="noshade"/ color="#d0e0f0" width="100%"> </td> </tr> </table>  <script type="text/javascript" src="https://www.informatics.jax.org/webshare/js/mgi_template01.js"></script> <script type="text/javascript" src="https://www.informatics.jax.org/webshare/js/mgi_ga.js"></script> <script> // For some pages (like HMDC Home) that don't have a templateBodyInsert element, we don't want to do this as it // presents an odd error popup. if (document.getElementById('templateBodyInsert') != null) { setTimeout(function() { overlib('Building initial tooltip...',ANCHOR, 'templateBodyInsert', ANCHORALIGN, 'UR', 'UL'); 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align-items: center; -ms-flex-line-pack: justify; align-content: space-between } .ccb-button { margin: 0 10px 0 0; -webkit-transition: all 100ms ease-in-out; transition: all 100ms ease-in-out; } .ccb-button:last-child { margin: 0; } .ccb-button:hover { cursor: pointer; } .ccb-button.allow{ background: #002255; color: #fff; padding: 10px 20px; border-radius: 3px; } .ccb-button.allow:hover{ background: green; } @media print { .ccb-panel { display: none } } </style> <div id="ccBanner" class="ccb-panel" > <div class="ccb-tag">  <svg name="uparrow" mlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#fff"><path d="m256-424-56-56 280-280 280 280-56 56-224-223-224 223Z"/></svg>  <svg name="downarrow" xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#fff"><path d="M480-345 240-585l56-56 184 183 184-183 56 56-240 240Z"/></svg> </div> <div class="ccb-body" role="dialog" aria-live="polite" aria-label="cookieconsent" aria-describedby="cookieconsent">  <div class="message"> This site uses cookies. 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