https://sourceforge.net/p/altanalyze/wiki/SubgeneViewer/Recent changes to SubgeneViewerenSat, 01 Feb 2014 01:06:43 -0000https://sourceforge.net/p/altanalyze/wiki/SubgeneViewer/<div class="markdown_content"><h2 id="subgeneviewer-10"><a class="" href="/p/altanalyze/wiki/SubgeneViewer/">SubgeneViewer</a> 1.0</h2> <p><a class="" href="/p/altanalyze/wiki/SubgeneViewer/">SubgeneViewer</a> is a plugin in development for the network visualization software Cytoscape. Slated to be released as a part of GenMAPP-CS beta in late 2012, <a class="" href="/p/altanalyze/wiki/SubgeneViewer/">SubgeneViewer</a> allows users to examine the complete exon, junction and intron structure of a gene and view associated exon expression data. Annotations for <a class="" href="/p/altanalyze/wiki/SubgeneViewer/">SubgeneViewer</a> are derived from <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a> during the database build process. </p> <p><a href="http://dx.plos.org/10.1371/journal.pcbi.1000553" rel="nofollow">http://dx.plos.org/10.1371/journal.pcbi.1000553</a></p> <h2 id="subgeneviewer-20"><a class="" href="/p/altanalyze/wiki/SubgeneViewer/">SubgeneViewer</a> 2.0</h2> <p><a class="" href="/p/altanalyze/wiki/SubgeneViewer/">SubgeneViewer</a> 2.0 will be implemented with data from RNASeq experiments in mind. Specifically, novel exon and junction information will be included in the existing gene model (meta-transcript view) and new view analagous to that provided in <a class="" href="../DomainGraph">DomainGraph</a> will be implemented (multi-transcript view). The multi-transcript view will allow users to visualize the impact of alternative exon and junction expression protein domain, motifs and microRNA binding sites. Both known and novel transcripts detected in a user's experiment will be supported (see below mockup). </p> <p><img alt="" src="http://altanalyze.org/image/SGV2_mockup.jpg" rel="nofollow" /></p> <p>Mockup of the (A) meta-transcript and (B) multi-transcript views in <a class="" href="/p/altanalyze/wiki/SubgeneViewer/">SubgeneViewer</a> 2.0. </p></div>AnonymousSat, 01 Feb 2014 01:06:43 -0000https://sourceforge.net10bf7c1a4d0262873451ee0e643862d541344b5d