https://wiki.genometracker.org/index.php?action=history&feed=atom&title=Carmen-Proteomics 2026-05-27T21:30:38Z Revision history for this page on the wiki MediaWiki 1.39.2 https://wiki.genometracker.org/index.php?title=Carmen-Proteomics&diff=4689&oldid=prev 2017-03-22T14:06:58Z

<p><span dir="auto"><span class="autocomment">Tuesday, March 21, 2017</span></span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:06, 22 March 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2">Line 2:</td> <td colspan="2" class="diff-lineno">Line 2:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Preliminary results of GSEA runs by Amanda Larracuente (Qiu Lab)</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Preliminary results of GSEA runs by Amanda Larracuente (Qiu Lab)</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Methods</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Methods</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div># Rank identified proteins by t-statistics, which is a measure of difference between WT and KO mice (3 individuals each). Most genes don&#039;t change, with t close to zero. t &lt;&lt; 0 suggests down-regulation in KO mice relative to WT mice, and t &gt;&gt; 0 suggests up-regulation. (Need to <del style="font-weight: bold; text-decoration: none;">make sure of the sign</del>)</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div># Rank identified proteins by t-statistics, which is a measure of difference between WT and KO mice (3 individuals each). Most genes don&#039;t change, with t close to zero. t &lt;&lt; 0 suggests down-regulation in KO mice relative to WT mice, and t &gt;&gt; 0 suggests up-regulation. (<ins style="font-weight: bold; text-decoration: none;">Could be the other way around. </ins>Need to <ins style="font-weight: bold; text-decoration: none;">confirm</ins>)</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Download mice gene sets from a web resource</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Download mice gene sets from a web resource</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Run GSEA by Broad Institute</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Run GSEA by Broad Institute</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893 Results using mice gene set with GO annotations]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893 Results using mice gene set with GO annotations]</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations]</div></td></tr> <!-- diff cache key my_wiki:diff::1.12:old-4688:rev-4689 --> </table>

imported>Weigang https://wiki.genometracker.org/index.php?title=Carmen-Proteomics&diff=4688&oldid=prev 2017-03-22T03:12:09Z

<p><span dir="auto"><span class="autocomment">Tuesday, March 21, 2017</span></span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:12, 22 March 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Download mice gene sets from a web resource</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Download mice gene sets from a web resource</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Run GSEA by Broad Institute</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Run GSEA by Broad Institute</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893 <del style="font-weight: bold; text-decoration: none;">| </del>Results using mice gene set with GO annotations]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893 Results using mice gene set with GO annotations]</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations]</div></td></tr> </table>

imported>Weigang https://wiki.genometracker.org/index.php?title=Carmen-Proteomics&diff=4687&oldid=prev 2017-03-22T03:11:53Z

<p><span dir="auto"><span class="autocomment">Tuesday, March 21, 2017</span></span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:11, 22 March 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Download mice gene sets from a web resource</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Download mice gene sets from a web resource</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Run GSEA by Broad Institute</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Run GSEA by Broad Institute</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* <del style="font-weight: bold; text-decoration: none;">[</del>[http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893 | Results using mice gene set with GO annotations<del style="font-weight: bold; text-decoration: none;">]</del>]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893 | Results using mice gene set with GO annotations]</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations]</div></td></tr> </table>

imported>Weigang https://wiki.genometracker.org/index.php?title=Carmen-Proteomics&diff=4686&oldid=prev 2017-03-22T03:11:38Z

<p><span dir="auto"><span class="autocomment">Tuesday, March 21, 2017</span></span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:11, 22 March 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Download mice gene sets from a web resource</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Download mice gene sets from a web resource</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Run GSEA by Broad Institute</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Run GSEA by Broad Institute</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [[<del style="font-weight: bold; text-decoration: none;">Results using mice gene set with GO annotations|</del>http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893]]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [[http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893 <ins style="font-weight: bold; text-decoration: none;">| Results using mice gene set with GO annotations</ins>]]</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations]</div></td></tr> </table>

imported>Weigang https://wiki.genometracker.org/index.php?title=Carmen-Proteomics&diff=4685&oldid=prev 2017-03-22T03:10:35Z

<p>Created page with &quot;=Tuesday, March 21, 2017= Preliminary results of GSEA runs by Amanda Larracuente (Qiu Lab) * Methods # Rank identified proteins by t-statistics, which is a measure of differen...&quot;</p> <p><b>New page</b></p><div>=Tuesday, March 21, 2017=<br /> Preliminary results of GSEA runs by Amanda Larracuente (Qiu Lab)<br /> * Methods<br /> # Rank identified proteins by t-statistics, which is a measure of difference between WT and KO mice (3 individuals each). Most genes don&#039;t change, with t close to zero. t &lt;&lt; 0 suggests down-regulation in KO mice relative to WT mice, and t &gt;&gt; 0 suggests up-regulation. (Need to make sure of the sign)<br /> # Download mice gene sets from a web resource<br /> # Run GSEA by Broad Institute<br /> * [[Results using mice gene set with GO annotations|http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893]]<br /> * [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations]</div>

imported>Weigang