8c2f7318d8d821de9b2a25750586a94ab5e8c1bb lrnassar Fri Nov 15 18:50:19 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/fantom5.html src/hg/makeDb/trackDb/fantom5.html index d1eab36..4d699ce 100644 --- src/hg/makeDb/trackDb/fantom5.html +++ src/hg/makeDb/trackDb/fantom5.html @@ -87,33 +87,33 @@ <a href="../../goldenPath/help/api.html">REST API</a>. ReMap annotations can be downloaded from the <a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/reMap">Genome Browser's download server</a> as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large.</p> <p> The FANTOM5 reprocessed data can be found and downloaded on the <a href="https://fantom.gsc.riken.jp/5/datafiles/reprocessed/" target="_blank">FANTOM website.</a></p> <h2>Credits</h2> <p> Thanks to Shuhei Noguchi, the <a href="https://fantom.gsc.riken.jp/5/" target=_blank>FANTOM5 consortium</a>, the Large Scale Data Managing Unit and Preventive Medicine and -Applied Genomics Unit, the <a href="http://www.riken.jp/en/research/labs/ims/" +Applied Genomics Unit, the <a href="https://www.riken.jp/en/research/labs/ims/" target=_blank>Center for Integrative Medical Sciences (IMS)</a>, and -<a href="http://www.riken.jp/" target=_blank>RIKEN</a> for providing this data +<a href="https://www.riken.jp/" target=_blank>RIKEN</a> for providing this data and its analysis.</p> <h2>References</h2> <p> Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T <em>et al</em>. <a href="https://doi.org/10.1038/nature12787" target="_blank"> An atlas of active enhancers across human cell types and tissues</a>. <em>Nature</em>. 2014 Mar 27;507(7493):455-461. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24670763" target="_blank">24670763</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215096/" target="_blank">PMC5215096</a> </p> <p> Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M @@ -126,31 +126,31 @@ </p> <p> FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M <em>et al</em>. <a href="https://doi.org/10.1038/nature13182" target="_blank"> A promoter-level mammalian expression atlas</a>. <em>Nature</em>. 2014 Mar 27;507(7493):462-70. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24670764" target="_blank">24670764</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748/" target="_blank">PMC4529748</a> </p> <p> Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO <em>et al</em>. -<a href="http://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=21596820" target="_blank"> +<a href="https://genome.cshlp.org/cgi/content/long/" target="_blank"> Unamplified cap analysis of gene expression on a single-molecule sequencer</a>. <em>Genome Res</em>. 2011 Jul;21(7):1150-9. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21596820" target="_blank">21596820</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129257/" target="_blank">PMC3129257</a> </p> <p> Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S <em>et al</em>. <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0560-6" target="_blank"> Gateways to the FANTOM5 promoter level mammalian expression atlas</a>. <em>Genome Biol</em>. 2015 Jan 5;16(1):22. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25723102" target="_blank">25723102</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310165/" target="_blank">PMC4310165</a>