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/mouse/rikenCageCtss.html src/hg/makeDb/trackDb/mouse/rikenCageCtss.html
index d7e2a81cf0a..26d32b4c342 100644
--- src/hg/makeDb/trackDb/mouse/rikenCageCtss.html
+++ src/hg/makeDb/trackDb/mouse/rikenCageCtss.html
@@ -33,31 +33,31 @@
 of the resulting 32 bp tags were then formed for more efficient sequencing.
 A total of 7,151,511 mapped CAGE tags from 145 cDNA libraries, corresponding to 
 22 distinct tissues were produced. 
 The tags were mapped to the mm5 assembly and lifted to other
 assemblies using UCSC's liftOver tool.
 For more information on
 CAGE, see Shiraki <em>et al.</em> (2003) and Carninci <EM>et al</EM> (2005)
 below.  The mapping methodology employed in this annotation 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/" TARGET=_blank>FANTOM</A>)
 Consortium, RIKEN Genome Science Laboratory and
-<A HREF="http://genome.gsc.riken.go.jp/home.html" TARGET=_blank>
+<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.