9ed3e168a16f43599dd0e095304e54e049d99294 jnavarr5 Mon Jun 16 13:58:13 2025 -0700 Creating links to the download files in the Methods section for the Unusual Conservation track for hg38, refs #35703 diff --git src/hg/makeDb/trackDb/human/hg38/unusualcons.html src/hg/makeDb/trackDb/human/hg38/unusualcons.html index 0f7814454e3..1c95fc61f96 100644 --- src/hg/makeDb/trackDb/human/hg38/unusualcons.html +++ src/hg/makeDb/trackDb/human/hg38/unusualcons.html @@ -124,49 +124,65 @@ <h2>Display Conventions and Configuration</h2> <p>All tracks show the locations and name for the features. Only one, Short hCondels, has MPRA test results in the track itself. </p> <h2>Methods</h2> <p>Ultraconserved sequences: downloaded from our hg19 public track hub and lifted to hg38. </p> <p> HARs: Downloaded from <a target=_blank href="https://docpollard.org/research/">https://docpollard.org/research/</a>. Converted from Excel. Lifted 2649 HAR file to hg38. </p> <p> -HAQERs: Converted from supplemental table 1 of (Mangan et al, Cell 2023). +HAQERs: Converted from supplemental table 1 of +(<a href="https://www.cell.com/cell/fulltext/S0092-8674(22)01358-7" +target="_blank">Mangan et al, Cell 2023</a>). </p> <p> -Long hCondels from McLean: Excel file converted manually as supplement 2 from https://pmc.ncbi.nlm.nih.gov/articles/PMC3071156/ and lifted to hg38 from hg18. +Long hCondels from McLean: Excel file converted manually as supplement 2 from +<a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3071156/" +target="_blank">https://pmc.ncbi.nlm.nih.gov/articles/PMC3071156/</a> and lifted to hg38 from hg18. </p> <p> Short hCondels from Xue et al: Excel file converted manually from supplemental file 1. -From the paper: "We constructed a chimpanzee-anchored multiple sequence alignment across 11 vertebrate species to detect statistically significant conserved sequences (1,371,766). These elements ranged from being deeply conserved throughout vertebrates to being conserved only through primates. We then intersected our conserved elements with called deletions (2,042,706) between the human (hg38) and chimpanzee (panTro4) genomes to yield 43,588 putative hCONDELs." +From the paper: "We constructed a chimpanzee-anchored multiple sequence alignment across 11 +vertebrate species to detect statistically significant conserved sequences (1,371,766). These +elements ranged from being deeply conserved throughout vertebrates to being conserved only through +primates. We then intersected our conserved elements with called deletions (2,042,706) between the +human (hg38) and chimpanzee (panTro4) genomes to yield 43,588 putative hCONDELs." </p> <p> -Zoonomia UNICORNs, ZooUCEs and RoCCs: Downloaded from https://cgl.gi.ucsc.edu/data/cactus/zoonomia-2021-track-hub/hg38/ +Zoonomia UNICORNs, ZooUCEs and RoCCs: Downloaded from +<a href="https://cgl.gi.ucsc.edu/data/cactus/zoonomia-2021-track-hub/hg38/" +target="_blank">https://cgl.gi.ucsc.edu/data/cactus/zoonomia-2021-track-hub/hg38/</a> <p> <h2>Credits</h2> -<p>Thanks to Katie Pollard, Hiram Clawson, James Xue, Matt Christmas (matthew.christmas@imbim.uu.se), and Mark Diekhans for providing the data.</p> +<p> +Thanks to Katie Pollard, Hiram Clawson, James Xue, Matt Christmas +(<A HREF="mailto:matthew. +christmas@imbim. +uu.se" +>matthew.christmas@imbim.uu.se</A>), +and Mark Diekhans for providing the data.</p> <h2>References</h2> <p> Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. <a href="https://www.science.org/doi/10.1126/science.1098119?url_ver=Z39.88-2003&rfr_id=ori:rid: crossref.org&rfr_dat=cr_pub%20%200pubmed" target="_blank"> Ultraconserved elements in the human genome</a>. <em>Science</em>. 2004 May 28;304(5675):1321-5. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15131266" target="_blank">15131266</a> </p> <p> Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C,