c2e552afa0d0574db2c2d93b51cd87b6484c4ddb jnavarr5 Fri Jun 13 15:59:17 2025 -0700 Adding links to the papers mentioned in the description for each track, refs #35703 diff --git src/hg/makeDb/trackDb/human/hg38/unusualcons.html src/hg/makeDb/trackDb/human/hg38/unusualcons.html index 746e69e7aba..0f7814454e3 100644 --- src/hg/makeDb/trackDb/human/hg38/unusualcons.html +++ src/hg/makeDb/trackDb/human/hg38/unusualcons.html @@ -1,54 +1,69 @@ <h2>Description</h2> <p>These tracks show regions of unusual conservation in human relative to other organisms:</p> <ul> <li><b>Ultraconserved elements (UCE aka ultras):</b><br> - Elements with 100% identity in human/mouse/rat alignments, from (Bejerano et al, Science 2004). - Many of these were tested in mice, see the VISTA enhancers track in the Regulation track group. + Elements with 100% identity in human/mouse/rat alignments. Many of these were tested in mice, + see the <a href="/cgi-bin/hgTrackUi?db=hg38&g=vistaEnhancersBb">VISTA enhancers</a> track in + the Regulation track group. (<a href="https://www.science.org/doi/10.1126/science.1098119" + target="_blank">Bejerano et al, Science 2004</a>) <li><b>Human Accelerated Regions (HARs):</b><br> - 2649 regions conserved throughout vertebrate evolution but strikingly different in humans (Pollard et al, Nature 2006). - This extended list was collected by the Katie Pollard lab from various publications (Capra et al. PTRSB 2013). + 2,649 regions conserved throughout vertebrate evolution but strikingly different in humans + (<a href="https://www.nature.com/articles/nature05113" target="_blank">Pollard et al, Nature + 2006</a>). + This extended list was collected by the Katie Pollard lab from various publications + (<a href="https://royalsocietypublishing.org/doi/full/10.1098/rstb.2013.0025" + target="_blank">Capra et al. PTRSB 2013</a>). <li><b>High-confidence Zoonomia Human Accelerated Regions (HARs):</b><br> - 312 HARs from the Zoonomia Alignments (Keough et al. Science, 2023) + 312 HARs from the Zoonomia Alignments (<a href="https://www.science.org/doi/abs/10.1126/science.abm1696" + target="_blank">Keough et al. Science, 2023</a>) <li><b>Human Ancestor Quickly Evolved Regions (HAQERs):</b><br> - 1580 HAQERs from (Mangan Cell 2023) + 1,580 HAQERs from (<a href="https://www.cell.com/cell/fulltext/S0092-8674(22)01358-7" + target="_blank">Mangan Cell 2023</a>) <li><b>Human-specific long deletions (hCondels) between human, macaque and chimpanzee:</b><br> - 583 regions (one not lifted) present in macaque and chimp, but no in humans. (McLean et al Nature 2011) - Since these are sequences absent from the human genome, we show the 2bp around the deletion. + 583 regions (one not lifted) present in macaque and chimp, but no in humans. Since these are + sequences absent from the human genome, we show the 2bp around the deletion. + (<a href="https://www.nature.com/articles/nature09774" + target="_blank">McLean et al Nature 2011</a>) <li><b>Short hCondels < 40bp in primates and up to 11 vertebrates:</b><br> - 43588 regions deleted in human but present in 11 vertebrates or primates from (Xue et al, Science 2023). These regions were tested - in an MPRA screen, the MPRA results are in the track and shown when clicking an element. Since the track is showing MPRA results - and the position of deletions, what is shown in the track are regions +-100bp around the deletion site on the human genome, - not just the two basepairs flanking the site of the deletion. + 43,588 regions deleted in human but present in 11 vertebrates or primates. These regions were + tested in an MPRA screen, the MPRA results are in the track and shown when clicking an element. + Since the track is showing MPRA results and the position of deletions, what is shown in the + track are regions ±100bp around the deletion site on the human genome, not just the two + basepairs flanking the site of the deletion. (<a href="https://www.science.org/doi/abs/10.1126/science.abn2253" + target="_blank">Xue et al, Science 2023</a>) <li><b>Zoonomia Ultraconserved elements (zooUCEs):</b><br> - 4552 Ultraconserved elements identified from the 241-mammals genome alignment. All regions >=20bp where - at least 235 species aligned and all aligning species are fixed for the same base at every position. 20-190 bp. + 4,552 Ultraconserved elements identified from the 241-mammals genome alignment. All regions + >=20bp where at least 235 species aligned and all aligning species are fixed for the same + base at every position. 20-190 bp. <li><b>Zoonomia: Runs of contiguous constraint (RoCCs):</b><br> All genomic regions where contiguous bases have phyloP score > 2.270 (5% FDR) and are therefore under high constraint. Regions separated by a single base with phyloP < 2.270 were merged. N = 595,535; 20-1,359 bp. <li><b>Zoonomia: Unannotated Intergenic Constrained Regions (UNICORNs):</b><br> Non-coding regions of the genome that lack annotation in ENCODE3 but show high evolutionary constraint, suggesting function. Positions with phyloP > 2.270 (5% FDR) within 5bp of each other are grouped into UNICORNs. N = 424,180; 11 - 1,325 bp. - <li><b>UCNEBase: Elements conserved with chicken from (Dimitrieva and Bucher, NAR 2013):</b><br> - non-coding elements > 200 bp long and 95% conserved between human and chicken + <li><b>UCNEBase: Elements conserved with chicken:</b><br> + Non-coding elements > 200 bp long and 95% conserved between human and chicken. + (<a href="https://academic.oup.com/nar/article/41/D1/D101/1057253" + target="_blank">Dimitrieva and Bucher, NAR 2013</a>) <li><b>UCNEBase: Elements paralogous to others:</b><br> - alignable with E<10<sup>-4</sup> to other chicken-conserved elements + Alignable with E<10<sup>-4</sup> to other chicken-conserved elements. <li><b>UCNEBase UGRBs: Ultra-conserved genomic regulatory blocks:</b><br> - chicken-conserved elements within 0.5 Mb in both human and chicken + Chicken-conserved elements within 0.5 Mb in both human and chicken. </ul> <table class="stdTbl"> <tr> <th>Track</th> <th>Count</th> <th>Coverage in bp</th> </tr> <tr> <td>Ultraconserved</td> <td>481</td> <td>126,007</td> </tr> <tr> <td>UCNEBase Chicken</td>