089c09e98db52e92da694ab1a0c8891c1a7fd3e8 gperez2 Thu Apr 2 15:50:07 2026 -0700 Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM. diff --git src/hg/makeDb/trackDb/human/affyHuEx1.html src/hg/makeDb/trackDb/human/affyHuEx1.html index 6bdea49eb03..b022183c7b6 100644 --- src/hg/makeDb/trackDb/human/affyHuEx1.html +++ src/hg/makeDb/trackDb/human/affyHuEx1.html @@ -1,111 +1,111 @@ <H2>Description</H2> <P> -The <A HREF="http://www.affymetrix.com/estore/browse/products.jsp?navMode= +The <A HREF="https://www.affymetrix.com/estore/browse/products.jsp?navMode= 34000&productId=131452&navAction=jump&aId=productsNav#1_1" TARGET=_blank>Human Exon 1.0 ST</A> GeneChip contains over 1.4 million probe sets designed to interrogate individual exons rather than the 3' ends of transcripts as in traditional GeneChips. Exons were derived from a variety of annotations that have been divided into the classes Core, Extended and Full. <UL> <LI><B>Core: </B>RefSeq transcripts, full-length GenBank mRNAs</LI> <LI><B>Extended:</B> dbEst alignments, Ensembl annotations, syntenic mRNA from rat and mouse, microRNA annotations, MITOMAP annotations, Vega genes, Vega pseudogenes <LI><B>Full:</B> Geneid genes, Genscan genes, Genscan Subopt, Exoniphy, RNA genes, SGP genes, Twinscan genes </LI> </UL></P> <P> Probe sets are colored by class with the Core probe sets being the darkest and the Full being the lightest color. Additionally, probe sets that do not overlap the exons of a transcript cluster, but fall inside of its introns, are considered bounded by that transcript cluster and are colored slightly lighter. Probe sets that overlap the coding portion of the Core class are colored slightly darker.</P> <P> The microarray track using this probe set can be displayed by turning on the <B>Affy All Exon</B> track.</P> <H2>Credits and References</H2> <P> The exons interrogated by the probe sets displayed in this track are from the Affymetrix Human Exon 1.0 GeneChip and were derived from a number of sources. In addition to the millions of cDNA sequences contributed to the <A HREF="https://www.ncbi.nlm.nih.gov/Genbank/index.html" TARGET=_blank>GenBank</A>, <A HREF="https://www.ncbi.nlm.nih.gov/dbEST/" TARGET=_blank>dbEst</A> and <A HREF="https://www.ncbi.nlm.nih.gov/RefSeq/" TARGET=_blank>RefSeq</A> databases by individual labs and scientists, the following annotations were used: <P> -<A HREF="http://www.ensembl.org/index.html" +<A HREF="https://www.ensembl.org/index.html" TARGET=_blank><B>Ensembl</B></A><B>: </B> Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T <em>et al.</em>. <A HREF="https://academic.oup.com/nar/article/30/1/38/1332872" TARGET=_blank>The Ensembl genome database project</A>. <em>Nucleic Acids Research</em>. 2002 Jan 1;30(1):38-41.</P> <P> <B>Exoniphy:</B> Siepel, A., Haussler, D. -<A HREF="http://compgen.cshl.edu/~acs/recomb2004.pdf" +<A HREF="https://doi.org/10.1101/gr.3715005" TARGET=_blank>Computational identification of evolutionarily conserved exons</A>. <em>Proc. 8th Int'l Conf. on Research in Computational Molecular Biology</em>, 177-186 (2004).</P> <P> <B><A HREF="https://genome.crg.es/geneid.html" TARGET=_blank>Geneid Genes</A>:</B> Parra, G., Blanco, E., Guigo, R. <A HREF="https://genome.cshlp.org/content/10/4/511.abstract" TARGET=_blank>Geneid in Drosophila</A>. <em>Genome Res.</em> <B>10</B>(4), 511-515 (2000).</P> <P> <B><A HREF="http://hollywood.mit.edu/GENSCAN.html" TARGET=_blank>Genscan Genes</A>: </B> Burge, C., Karlin, S. <A HREF="https://www.sciencedirect.com/science/article/pii/S0022283697909517" TARGET=_blank>Prediction of Complete Gene Structures in Human Genomic DNA</A>. <em>J. Mol. Biol.</em> <B>268</B>(1), 78-94 (1997).</P> <P> <B><A HREF="https://www.mirbase.org//ftp.shtml" TARGET=_blank>microRNA</A>: </B> Griffiths-Jones, S. <A HREF="https://academic.oup.com/nar/article/32/suppl_1/D109/2505171" TARGET=_blank>The microRNA Registry</A>. <em>Nucl. Acids Res.</em> <B>32</B>, D109-D111 (2004).</P> <P> <B><A HREF="https://www.mitomap.org/MITOMAP" TARGET=_blank>MITOMAP</A>: </B> Brandon, M. C., Lott, M. T., Nguyen, K. C., Spolim, S., Navathe, S. B., Baldi, P. & Wallace, D. C. <A HREF="https://academic.oup.com/nar/article/33/suppl_1/D611/2505354" TARGET=_blank>MITOMAP: a human mitochondrial genome database--2004 update</A> <em>Nucl. Acids Res.</em> <B>33</B>(Database Issue):D611-613 (2005). </P> <P> <B><A HREF="http://eddylab.org" TARGET=_blank>RNA Genes</A>: </B> Lowe, T. M., Eddy, S. R. <A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/" TARGET=_blank>tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence</A>. <em>Nucleic Acids Res.</em>, <B>25</B>(5), 955-964 (1997).</P> <P> <B><A HREF="https://grib.upf.edu/" TARGET=_blank>SGP Genes</A>: </B> Wiehe, T., Gebauer-Jung, S., Mitchell-Olds, T., Guigo, R. <A HREF="https://genome.cshlp.org/content/11/9/1574.abstract" TARGET=_blank>SGP-1: prediction and validation of homologous genes based on sequence alignments</A>. <em>Genome Res.</em>, <B>11</B>(9), 1574-83 (2001).</P> <P> <B><A HREF="https://mblab.wustl.edu/" TARGET=_blank>Twinscan Genes</A>: </B> Korf, I., Flicek, P., Duan, D., Brent, M.R. <A HREF="https://academic.oup.com/bioinformatics/article/17/suppl_1/S140/261903" TARGET=_blank>Integrating genomic homology into gene structure prediction</A>. <em>Bioinformatics</em> 17, S140-148 (2001). <P> <B><A HREF="http://vega.archive.ensembl.org/index.html" TARGET=_blank>Vega Genes and Pseudogenes</A>: </B>The HAVANA group, <A HREF="https://www.sanger.ac.uk/" TARGET=_blank>Wellcome Trust Sanger Institute</A>.</P>