38aed9a87ffb6dfe6550f81318e4989c209ec0d1 jnavarr5 Tue Apr 30 09:29:58 2019 -0700 Updating http to https for mm7, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/mouse/rikenCageCtss.html src/hg/makeDb/trackDb/mouse/rikenCageCtss.html index c623091..b8c8d12 100644 --- src/hg/makeDb/trackDb/mouse/rikenCageCtss.html +++ src/hg/makeDb/trackDb/mouse/rikenCageCtss.html @@ -1,113 +1,113 @@ <H2>Description</H2> <P> This track shows the number of 5' cap analysis gene expression (CAGE) tags that map to the genome on the "plus" and "minus" 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. The number of tags should be proportional to the expression rate in the originating tissues.</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' CAGE tag starts that map at that location.</P> <P> This composite annotation track contains two 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> To create the tag, a linker was attached to the 5' end of full-length cDNAs which had been selected by cap trapping. The first 20 bp of the cDNA were cleaved using the class II restriction enzyme, MmeI, followed by PCR amplification. Concatamers 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="http://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> 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> Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C <em>et al</em>. -<a href="http://science.sciencemag.org/content/309/5740/1559" target="_blank"> +<a href="https://science.sciencemag.org/content/309/5740/1559" target="_blank"> The transcriptional landscape of the mammalian genome</a>. <em>Science</em>. 2005 Sep 2;309(5740):1559-63. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16141072" target="_blank">16141072</a> </p> <p> Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T <em>et al</em>. -<a href="http://www.pnas.org/content/100/26/15776" target="_blank"> +<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>. 2003 Dec 23;100(26):15776-81. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14663149" target="_blank">14663149</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC307644/" target="_blank">PMC307644</a> </p>