CHIP File Selection Help - Revision history https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=CHIP_File_Selection_Help&action=history Revision history for this page on the wiki en MediaWiki 1.34.4 Fri, 29 Mar 2024 14:11:25 GMT Acastanza at 17:12, 15 September 2022 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=CHIP_File_Selection_Help&diff=4511&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=CHIP_File_Selection_Help&diff=4511&oldid=prev <p></p> <table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:12, 15 September 2022</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l6" >Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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://www.broadinstitute.org/gsea/contact.jsp Contact]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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://www.broadinstitute.org/gsea/contact.jsp Contact]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>&lt;/span&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>&lt;/span&gt;</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;">The 4.3.0 version of GSEA introduced support for the new gene set database files and chip files to support native analysis of mouse data first made available with MSigDB v2022.1.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;">These files are now split into two different tabs in both the GSEA gene sets and chip files UI windows.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;">Gene set files from the Human Collections have the suffix &quot;.'''Hs'''.symbols.gmt&quot; following the MSigDB version (v2022.1 in this initial release), gene set files from the Mouse Collections have the suffix &quot;.'''Mm'''.symbols.gmt&quot;. Gene set files from the Human Collections have their contents provided in HGNC Gene Symbols, gene set files from the Mouse Collections have their contents provided in MGI Gene Symbols. These symbols follow different canonical formats (i.e. MTOR for human vs. Mtor for mouse). </ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;">As such, it is critical to pick CHIP files that map your data into the appropriate namespace (either human or mouse symbols).</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;">Therefore, if a gene set file from the ''Human Collection (MSigDB)'' window is selected, you must also select a CHIP file from the ''Human Collection Chips (MSigDB)'' tab of the Chip platform selector window, and if a gene set file from the ''Mouse Collection (MSigDB)'' window is selected, you must also select a CHIP file from the ''Mouse Collection Chips (MSigDB)'' tab of the Chip platform selector window.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;">Chip files, like gene set database files are versioned and have a species specific suffix, i.e. &quot;.'''Hs'''.chip&quot; following the MSigDB version (v2022.1 in this initial release) for files targeting the Human Collections, and &quot;.'''Mm'''.chip&quot; for files targeting the Mouse Collections.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;">Both Human Collection Chips, and Mouse Collection Chips contain a full complement of Chips for native as well as orthology based analysis. Chips from the Human Collection Chips tab (files ending in .Hs.chip) that begin with '''Human_''' convert human gene IDs to human symbols, files from this tab (still with the .Hs.chip suffix) that begin with ''Mouse_'' or ''Rat_'' will also have the text &quot;_Human_Orthologs_&quot; in the file name, and when used will apply orthology mapping data to convert the dataset to match the human gene symbols namespace of the MSigDB Human Collections database.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;">Likewise, chips from the Mouse Collection Chips tab (files ending in .Mm.chip) that begin with '''Mouse''' convert mouse gene IDs to mouse symbols, files from this tab (still with the .Mm.chip suffix) that begin with ''Human'' or ''Rat_'' will also have the text &quot;_Mouse_Orthologs_&quot; in the file name, and when used will apply orthology mapping data to convert the dataset to match the mouse gene symbols namespace of the MSigDB mouse Collections database.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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><ins style="font-weight: bold; text-decoration: none;">So, if the gene set database file ''c5.go.bp.v2022.1.Hs.symbols.gmt'' was selected from the Human Collection's tab, the appropriate CHIP file regardless of dataset species would be one of the ''_MSigDB.v.2022.1.Hs.chip'' files available from the Human Collection CHIPs (MSigDB) tab, and if the gene set database file ''m5.go.bp.v2022.1.Mm.symbols.gmt'' was selected from the Mouse Collection's tab the appropriate CHIP file regardless of dataset species would be one of the ''_MSigDB.v.2022.1.Mm.chip'' files available from the Mouse Collection CHIPs (MSigDB) tab.</ins></div></td></tr> </table> Thu, 15 Sep 2022 17:12:44 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:CHIP_File_Selection_Help Acastanza: Creating Page https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=CHIP_File_Selection_Help&diff=4488&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=CHIP_File_Selection_Help&diff=4488&oldid=prev <p>Creating Page</p> <p><b>New page</b></p><div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;</div> Thu, 18 Aug 2022 21:07:56 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:CHIP_File_Selection_Help