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/oreganno.html src/hg/makeDb/trackDb/oreganno.html index ca657c4..65de099 100644 --- src/hg/makeDb/trackDb/oreganno.html +++ src/hg/makeDb/trackDb/oreganno.html @@ -1,114 +1,114 @@ <H2>Description</H2> <P> This track displays literature-curated regulatory regions, transcription factor binding sites, and regulatory polymorphisms from <a href="http://www.oreganno.org/" target="_blank">ORegAnno</a> (Open Regulatory Annotation). For more detailed information on a particular regulatory element, follow the link to ORegAnno from the details page. <!-- <b><font color="666600">O</font><font color="CC0033">Reg</font><font color="BBBB55">Anno</font></b> (Open Regulatory Annotation). --> </P> <H2>Display Conventions and Configuration</H2> <p>The display may be filtered to show only selected region types, such as:</p> <ul style="background-color: #fff; padding: 10px 15px 10px 30px; display: inline; display: inline-block; -webkit-border-radius: 3px; -moz-border-radius: 3px; border-radius: 3px; border: 1px solid #c4c4c4;"> <li style="color: #56B4E9;">regulatory regions (shown in light blue)</li> <li style="color: #0072B2;">regulatory polymorphisms (shown in dark blue)</li> <li style="color: #E69F00;">transcription factor binding sites (shown in orange)</li> <li style="color: #D55E00;">regulatory haplotypes (shown in red)</li> <li style="color: #009E73;">miRNA binding sites (shown in blue-green)</li> </ul> <p>To exclude a region type, uncheck the appropriate box in the list at the top of the Track Settings page. </p> <H2>Methods</H2> <P> An ORegAnno record describes an experimentally proven and published regulatory region (promoter, enhancer, etc.), transcription factor binding site, or regulatory polymorphism. Each annotation must have the following attributes: <ul> <li>A stable ORegAnno identifier. <li>A valid taxonomy ID from the NCBI taxonomy database. <li>A valid PubMed reference. <li>A target gene that is either user-defined, in Entrez Gene or in EnsEMBL. <li>A sequence with at least 40 flanking bases (preferably more) to allow the site to be mapped to any release of an associated genome. <li>At least one piece of specific experimental evidence, including the biological technique used to discover the regulatory sequence. (Currently only the evidence subtypes are supplied with the UCSC track.) <li>A positive, neutral or negative outcome based on the experimental results from the primary reference. (Only records with a positive outcome are currently included in the UCSC track.) </ul> The following attributes are optionally included: <ul> <li>A transcription factor that is either user-defined, in Entrez Gene or in EnsEMBL. <li>A specific cell type for each piece of experimental evidence, using the eVOC cell type ontology. <li>A specific dataset identifier (e.g. the REDfly dataset) that allows external curators to manage particular annotation sets using ORegAnno's curation tools. <li>A "search space" sequence that specifies the region that was assayed, not just the regulatory sequence. <li>A dbSNP identifier and type of variant (germline, somatic or artificial) for regulatory polymorphisms. </ul> Mapping to genome coordinates is performed periodically to current genome builds by BLAST sequence alignment. The information provided in this track represents an abbreviated summary of the details for each ORegAnno record. Please visit the official ORegAnno entry (by clicking on the ORegAnno link on the details page of a specific regulatory element) for complete details such as evidence descriptions, comments, validation score history, etc. </P> <H2>Credits</H2> <P> ORegAnno core team and principal contacts: Stephen Montgomery, Obi Griffith, -and Steven Jones from <A HREF="http://www.bcgsc.ca/" +and Steven Jones from <A HREF="https://www.bcgsc.ca/" TARGET=_blank>Canada's Michael Smith Genome Sciences Centre</A>, Vancouver, British Columbia, Canada.</P> <P> The ORegAnno community (please see individual citations for various features): <A HREF="http://www.oreganno.org/" TARGET="_blank">ORegAnno Citation</A>. <H2>References</H2> <p> Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL, Open Regulatory Annotation Consortium.. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1203" target="_blank"> ORegAnno 3.0: a community-driven resource for curated regulatory annotation</a>. <em>Nucleic Acids Res</em>. 2016 Jan 4;44(D1):D126-32. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26578589" target="_blank">26578589</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702855/" target="_blank">PMC4702855</a> </p> <p> Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M <em>et al</em>. <a href="https://academic.oup.com/nar/article/36/suppl_1/D107/2508119/ORegAnno-an-open-access- community-driven-resource" target="_blank"> ORegAnno: an open-access community-driven resource for regulatory annotation</a>. <em>Nucleic Acids Res</em>. 2008 Jan;36(Database issue):D107-13. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18006570" target="_blank">18006570</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2239002/" target="_blank">PMC2239002</a> </p> <P> Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. <A HREF="https://academic.oup.com/bioinformatics/article/22/5/637/206022/ORegAnno-an-open-access- database-and-curation" TARGET="_blank">ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation</A>. <em>Bioinformatics</em>. 2006 Mar 1;22(5):637-40. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16397004" target="_blank">16397004</a> </p>