ca02a0d7688a48a60418e217d89f162ca95f6fe2 jnavarr5 Tue Apr 13 14:44:54 2021 -0700 Fixing a link to the wrong track in a past news entry. Announcing the haploinsufficiency track for hg19, refs #25707 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 0456ff1..54518a2 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,61 @@ </div> <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> +<a name="041321"></a> +<h2>Apr. 13, 2021 New Haploinsufficiency predictions for human (hg19)</h2> +<p> +We are happy to announce a new haploinsufficiency predicitons track for human assembly +<a href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=decipherHaploIns">GRCh37/hg19</a>. This track displays +haploinsufficiency predictions for human genes from +<a href="https://www.deciphergenomics.org/" target="_blank">DECIPHER</a>. Human cells have two +copies of most genes, one from each parent. If a mutation alters one allele, or copy, the other is +usually still sufficient to maintain proper gene function. For haploinsufficient genes, however, +both copies must be functioning for the organism to have a normal life. Haploinsufficiency is +implicated in a number of health disorders. +</p> +<p> +Moving the mouse cursor over any gene in the track will display a pop-up box with the gene name +and α-upper quantile for the prediction. The genes in this track are also color-coded +according to quantile: +</p> +<ul> + <li> + <b><span style='color: #AA00AA'>Magenta</span></b> shades indicate a higher expectation of being + haploinsufficient</li> + <li> + <b><span style='color: #00AA00'>Green</span></b> shades indicate a lower expectation of being + haploinsufficient</li> +</ul> +<p> +We would like to thank the DECIPHER team for making the haploinsufficiency prediction data +available. We also want to thank Jonathan Casper and Jairo Navarro for the creation and release of +this track. +</p> + <a name="040121"></a> <h2>Apr. 01, 2021 Update to sno/miRNA track for human (hg19)</h2> <p> We are happy to announce an update to the sno/miRNA track for human assembly <a href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=wgRna">GRCh37/hg19</a>. With this update, the miRBase database was updated to version 20. The four different types of RNA and their counts in the human genome are listed below. </p> <ul> <li> C/D box small nucleolar RNAs (C/D box snoRNAs): 269</li> <li> H/ACA box snoRNAs: 112</li> <li> precursor forms of microRNAs (pre-miRNAs): 1871</li> @@ -1217,31 +1248,31 @@ PhyloCSF Rejected Genes</a> - This track shows other genes that have been proposed that do not show the signature of conserved protein-coding genes or persuasive experimental evidence, and are thus unlikely to be actual protein-coding genes, namely ORF3d, ORF3b, ORF14 (a.k.a. ORF9b, ORF9c), and ORF10.</li></ul> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=weizmanOrfs"> New ORFs based on RNA-seq and Ribo-seq by the Weizman Institute tracks</a> - The Weizman ORFs (Open Reading Frames) track shows previously unannotated ORF predictions based on Ribo-Seq and RNA-seq data. It contains four tracks comprised of the predicted gene models, and data supporting them.</li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=icshape"> icSHAPE RNA Structure</a> - This track shows normalized icSHAPE reactivity data of in vivo and in vitro SARS-CoV-2 experiments.</li> <li> -<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=icshape"> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=iedb"> Validated epitopes from IEDB</a> - This track shows epitope sequences displayed by various class I MHC alleles as annotated by National Institute for Allergy and Infectious Diseases (NIAID) <a href="https://www.iedb.org/" target="_blank"> Immune Epitope Database (IEDB)</a>.</li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=potPathoIndel"> Potential pathogenic insertions and deletions from Gussow <em>et al</em>, PNAS 2020</a> - This track shows genomic features that differentiate SARS-CoV-2 and the viruses behind the two previous deadly coronavirus outbreaks, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), from less pathogenic coronaviruses.</li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=pond"> Natural selection analysis from Sergei Pond's research group</a> - This track shows data from Pond <em>et al</em>, 2020 "Natural selection analysis of SARS-CoV-2/COVID-19" where authors used several statistical techniques to