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/encodeRikenCage.html src/hg/makeDb/trackDb/human/encodeRikenCage.html
index 9fb547e7fa1..67b2140a818 100644
--- src/hg/makeDb/trackDb/human/encodeRikenCage.html
+++ src/hg/makeDb/trackDb/human/encodeRikenCage.html
@@ -1,99 +1,99 @@
 <H2>Description</H2>
 <P>
 This track shows the number of 5' cap analysis gene expression (CAGE) tags 
 that map to the genome on the &quot;plus&quot; and &quot;minus&quot; strands at 
 a specific location.  For clarity, only the first 5' nucleotide in the tag 
 (relative to the transcript direction) is considered. Areas in which many tags 
 map to the same region may indicate a significant transcription start site.</P>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 The position of the first 5' nucleotide in the tag is represented by a solid
 block. The height of the block indicates the number of 5' cDNA starts that map
 at that location.</P>
 <P>
 This composite annotation track contains multiple subtracks that 
 may be configured in a variety of ways to highlight different aspects of the 
 displayed data. The graphical configuration options are shown at the top of 
 the track description page, followed by a list of subtracks.  
 For more information about the graphical configuration options, click the 
 <A HREF="../goldenPath/help/hgWiggleTrackHelp.html" TARGET=_blank>Graph
 configuration help</A> link. To display only selected subtracks, uncheck the 
 boxes next to the tracks you wish to hide. </P>
 
 <H2>Methods</H2>
 <P>
 The CAGE tags are sequenced from the 5' ends of full-length cDNAs produced using RIKEN full-length cDNA technology. To create the tag, a linker was 
 attached to the 5' end of full-length cDNAs which were selected by cap 
 trapping. The first 20 bp of the cDNA were cleaved using class II restriction 
 enzymes, followed by PCR amplification and then concatamers of the resulting
 32 bp tags were formed for more efficient sequencing. For more information on 
 CAGE analysis, see Shiraki <em>et al.</em> (2003) below. Refer to the 
-<A HREF="http://genome.gsc.riken.jp/home.html" TARGET=_blank>RIKEN</A> website
+<A HREF="https://www.riken.jp/en/" TARGET=_blank>RIKEN</A> website
 for information about RIKEN full-length cDNA technologies. The mapping 
 methodology employed in this annotation will be described in upcoming 
 publications.</P>
 
 <H2>Verification</H2>
 <P>
 The techniques used to verify these data will be described in upcoming 
 publications.</P>
 
 <H2>Credits</H2>
 <P>
 These data were contributed by the Functional Annotation of Mouse 
 (<A HREF="https://fantom.gsc.riken.jp/index.html" TARGET=_blank>FANTOM</A>) 
 Consortium, RIKEN Genome Science Laboratory and 
-<A HREF="http://genome.gsc.riken.jp/home.html" 
+<A HREF="https://www.riken.jp/en/" 
 TARGET=_blank>RIKEN Genome Exploration Research Group</A> 
 (Genome Network Project Core Group).</P>
 <P>
 <B>FANTOM Consortium:</B> P. Carninci, T. Kasukawa, S. Katayama, Gough, 
 M. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. 
 Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. 
 Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. Allen, 
 A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. 
 Bansal, K. W. Beisel, T. Bersano, H. Bono,  A. M. Chalk, K. P. Chiu, V. 
 Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, 
 B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, 
 P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, 
 M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, 
 T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, V. Harokopos, Y. 
 Hayashi, S. Henning, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, 
 M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. 
 Katoh, Y. Kawasawa, J. Kelso, H. Kitamura,  H. Kitano, G. Kollias, S. 
 P. T. Krishnan, A.F. Kruger, K. Kummerfeld, I. V. Kurochkin, 
 L. F. Lareau, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan 
 Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. 
 Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, 
 H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, 
 O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, 
 G. Pesole, N. Petrovsky, S. Piazza, W. Qu, J. Reed, J. F. Reid, B. Z. 
 Ring, M. Ringwald, B. Rost, Y. Ruan, S. Salzberg, A. Sandelin, C. 
 Schneider, C. Schoenbach, K. Sekiguchi, C. A. M. Semple, S. Seno, 
 L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, B. Sinclair, S. 
 Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. 
 Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, 
 H. R. Ueda, E. van Nimwegene, R. Verardo, C. L. Wei, K. Yagi, H. 
 Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. 
 Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. 
 Wahlestedt, J. Mattick, D. Hume. </P>
 <P>
 <B>RIKEN Genome Exploration Research Group:</B> C. Kai, D. Sasaki, Y. 
 Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. 
 Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato,  H. Kawaji, N. 
 Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. 
 Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. 
 Suzuki, M. Tagami, K Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. 
 Kawai. </P>
 <P>
 <B>General Organizer</B>: Y. Hayashizaki
 
 <H2>References</H2>
 <P>
 Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., 
 Kodzius, R., Watahiki, A., Nakamura, M. <em>et al</em>.
 <A HREF="https://www.pnas.org/content/100/26/15776"
 TARGET=_blank>Cap analysis gene expression for high-throughput analysis of 
 transcriptional starting point and identification of promoter usage</A>.
 <em>Proc Natl Acad Sci U S A.</em> <B>100</B>(26), 15776-81 (2003).</P>