http://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&feed=atom&action=historyDiG: Disease groups - Revision history2024-03-29T02:35:52ZRevision history for this page on the wikiMediaWiki 1.33.0http://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=3815&oldid=prevIan.donaldson: /* Introduction */2011-10-17T11:55:02Z<p><span dir="auto"><span class="autocomment">Introduction</span></span></p>
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<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>#a list of genes associated with genetic disorders</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>#a list of genes associated with genetic disorders</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>The human interaction network is taken from the [http://irefindex.uio.no iRefIndex] resource and the creation of the disease gene list is described on this page.</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>The human interaction network is taken from the [http://irefindex.uio.no iRefIndex] resource and the creation of the disease gene list is described on this page.</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;">Disease groups can be searched on using the iRefScape plugin for Cytoscape.</ins></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;"></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;"></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>=Method for sorting entries in Morbid Map into disease groups (DiG)=</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>=Method for sorting entries in Morbid Map into disease groups (DiG)=</div></td></tr>
</table>Ian.donaldsonhttp://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=987&oldid=prevIan.donaldson at 19:56, 6 April 20092009-04-06T19:56:42Z<p></p>
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<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;">[[Image:Vitruvian_man.jpg|right|Vitruvian man by Leonardo da Vinci]]</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 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>=Introduction=</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>=Introduction=</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>We investigate properties of human disease genes within the protein-protein interaction network. Two essential datasets are required for this research:</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>We investigate properties of human disease genes within the protein-protein interaction network. Two essential datasets are required for this research:</div></td></tr>
</table>Ian.donaldsonhttp://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=977&oldid=prevIan.donaldson at 17:15, 6 April 20092009-04-06T17:15:51Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:15, 6 April 2009</td>
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<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>=Availability=</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>=Availability=</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>DiG has not been published yet but can be made available to interested collaborators. Contact ian.donaldson@biotek.uio.no for more information.</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>DiG has not been published yet but can be made available to interested collaborators. Contact ian.donaldson@biotek.uio.no for more information.</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 DiG file format is described at http://donaldson.uio.no/wiki/README_DiG_1.0</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;">Sources used to build this data set are described at http://donaldson.uio.no/wiki/Sources_DiG_1.0</ins></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;"></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;"></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>=Reference=</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>=Reference=</div></td></tr>
</table>Ian.donaldsonhttp://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=976&oldid=prevIan.donaldson at 17:11, 6 April 20092009-04-06T17:11:27Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:11, 6 April 2009</td>
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<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </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>=Introduction=</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>=Introduction=</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>We investigate properties of human disease genes within the protein-protein interaction network. Two essential datasets are required for this research:</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>We investigate properties of human disease genes within the protein-protein interaction network. Two essential datasets are required for this research:</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l79" >Line 79:</td>
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<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>=Reference=</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>=Reference=</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><div id="ref1">1. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL, The human disease network. Proc Natl Acad Sci USA. 2007 May 22;104(21):8685-90 PMID 17502601</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><div id="ref1">1. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL, The human disease network. Proc Natl Acad Sci USA. 2007 May 22;104(21):8685-90 PMID 17502601</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;">[[Category:DiG]]</ins></div></td></tr>
</table>Ian.donaldsonhttp://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=962&oldid=prevIan.donaldson at 15:44, 6 April 20092009-04-06T15:44:56Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:44, 6 April 2009</td>
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<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">=Sorting entries in Morbid Map into disease groups=</del></div></td><td colspan="2"> </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;"></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;"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">=</del>=Introduction<del class="diffchange diffchange-inline">=</del>=</div></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>=Introduction=</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>We investigate properties of human disease genes within the protein-protein interaction network. Two essential datasets are required for this research:</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>We investigate properties of human disease genes within the protein-protein interaction network. Two essential datasets are required for this research:</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>#the human protein-protein interaction network and</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>#the human protein-protein interaction network and</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>#a list of genes associated with genetic disorders</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>#a list of genes associated with genetic disorders</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>The human interaction network is taken from the [http://irefindex.uio.no iRefIndex] resource and the creation of the disease gene list is described on this page.</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>The human interaction network is taken from the [http://irefindex.uio.no iRefIndex] resource and the creation of the disease gene list is described on this page.</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;">=Method for sorting entries in Morbid Map into disease groups (DiG)=</ins></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;"></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;"></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>==OMIM Morbid map==</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>==OMIM Morbid map==</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l59" >Line 59:</td>
<td colspan="2" class="diff-lineno">Line 60:</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>==Testing disease groups==</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>==Testing disease groups==</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>The publication from Goh et al. [[#ref1|[1]]] presented a similar effort in processing the Morbid Map. The Morbid Map release from December 2005 was processed by string matching to fuse sub-types of diseases. The original 2929 entries with disease tag “(3)” were grouped into 1284 groups and manually classified to 22 classes pointing to a physiological system affected in the human body. This publication was used to assess the accuracy of our disease grouping.</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>The publication from Goh et al. [[#ref1|[1]]] presented a similar effort in processing the Morbid Map. The Morbid Map release from December 2005 was processed by string matching to fuse sub-types of diseases. The original 2929 entries with disease tag “(3)” were grouped into 1284 groups and manually classified to 22 classes pointing to a physiological system affected in the human body. This publication was used to assess the accuracy of our disease grouping.</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The disease grouping of Goh et al. [[#ref1|[1]]] was transferred onto the August 2008 Morbid Map. This left about 400 newer entries unmatched. The groupings for the rest of the entries were compared (i.e. the genes that were mapped by both the Goh study and in our DiG list). In about 100 cases, DiG divisions were too conservative and groups needed to be fused. Sometimes the titles were not consistent between different entries in the Morbid Map. <del class="diffchange diffchange-inline">Inother </del>cases, the word order did not match or the most relevant word did not occur at the beginning of the title. Also, cancer names varied a lot. Most likely, Goh et al. manually intervened to sort out such groups. To deal with these inconsistent titles, new titles were created that could be processed correctly by the title matching parser and these to were added to the table prior to title matching. These new titles were often just variations on the original one, with a different word order or an extra comma. The changes to the titles were generated by a sql script and can be used on a new version of the Morbid Map to re-create the groups. The first version of this script contains about 150 sql statements.</div></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>The disease grouping of Goh et al. [[#ref1|[1]]] was transferred onto the August 2008 Morbid Map. This left about 400 newer entries unmatched. The groupings for the rest of the entries were compared (i.e. the genes that were mapped by both the Goh study and in our DiG list). In about 100 cases, DiG divisions were too conservative and groups needed to be fused. Sometimes the titles were not consistent between different entries in the Morbid Map. <ins class="diffchange diffchange-inline">In other </ins>cases, the word order did not match or the most relevant word did not occur at the beginning of the title. Also, cancer names varied a lot. Most likely, Goh et al. manually intervened to sort out such groups. To deal with these inconsistent titles, new titles were created that could be processed correctly by the title matching parser and these to were added to the table prior to title matching. These new titles were often just variations on the original one, with a different word order or an extra comma. The changes to the titles were generated by a sql script and can be used on a new version of the Morbid Map to re-create the groups. The first version of this script contains about 150 sql statements.</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>The total numbers of groups is about 1500. In the end, about 25 groups were deliberately kept more conservative than Goh et al.; i.e. one group by Goh et al. corresponds to two or more disease groups in DiG. In 25 cases, groups were fused that are separated in Goh et al. Overall, thorough manual checks were done '''ONLY''' on groups that were different between Goh et al. and DiG.</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>The total numbers of groups is about 1500. In the end, about 25 groups were deliberately kept more conservative than Goh et al.; i.e. one group by Goh et al. corresponds to two or more disease groups in DiG. In 25 cases, groups were fused that are separated in Goh et al. Overall, thorough manual checks were done '''ONLY''' on groups that were different between Goh et al. and DiG.</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;">=Description of DiG contents=</ins></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;"></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;"></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>==Multigenic groups of diseases==</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>==Multigenic groups of diseases==</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l68" >Line 68:</td>
<td colspan="2" class="diff-lineno">Line 71:</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>Currently, morbid map includes about 2200 distinct genes. 1400 of these are involved only in one disorder. The remaining 800 are implicated in two to 11 diseases. From this group, 58 genes are found connected to more than 5 disorders. The highest connected fraction (8 to 11 disorders, 14 instances) is enriched with tumor supressors (such as p53, PTEN, APC, KRAS), collagens and FGF receptors.</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>Currently, morbid map includes about 2200 distinct genes. 1400 of these are involved only in one disorder. The remaining 800 are implicated in two to 11 diseases. From this group, 58 genes are found connected to more than 5 disorders. The highest connected fraction (8 to 11 disorders, 14 instances) is enriched with tumor supressors (such as p53, PTEN, APC, KRAS), collagens and FGF receptors.</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;"></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;"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>==Reference<del class="diffchange diffchange-inline">=</del>=</div></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 class="diffchange diffchange-inline">Credits=</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 class="diffchange diffchange-inline">DiG was constructed by Katerina Michalickova in the Donaldson group at the Biotechnology Centre of Oslo.</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> </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 class="diffchange diffchange-inline">=Availability=</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 class="diffchange diffchange-inline">DiG has not been published yet but can be made available to interested collaborators. Contact ian.donaldson@biotek.uio.no for more information.</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> </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>=Reference=</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><div id="ref1">1. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL, The human disease network. Proc Natl Acad Sci USA. 2007 May 22;104(21):8685-90 PMID 17502601</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><div id="ref1">1. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL, The human disease network. Proc Natl Acad Sci USA. 2007 May 22;104(21):8685-90 PMID 17502601</div></td></tr>
</table>Ian.donaldsonhttp://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=961&oldid=prevIan.donaldson at 15:36, 6 April 20092009-04-06T15:36:52Z<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 15:36, 6 April 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l8" >Line 8:</td>
<td colspan="2" class="diff-lineno">Line 8:</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;"></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;"></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>==OMIM Morbid map==</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>==OMIM Morbid map==</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The largest and the most reliable disease association list is available from the Online Mendelian Inheritance in Man [http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim (OMIM) database]. The Morbid Map, maintained within this resource, lists gene and disease associations and is exported as simple table with about 5000 entries. Each line in this table corresponds to one gene – disorder association and looks as follows: <br/></div></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>The largest and the most reliable disease association list is available from the Online Mendelian Inheritance in Man [http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim (OMIM) database]. <ins class="diffchange diffchange-inline">[http://www.ncbi.nlm.nih.gov/Omim/getmorbid.cgi </ins>The Morbid Map<ins class="diffchange diffchange-inline">]</ins>, maintained within this resource, lists gene and <ins class="diffchange diffchange-inline">their </ins>disease associations and is exported as <ins class="diffchange diffchange-inline">a </ins>simple table with about 5000 entries. Each line in this table corresponds to one gene – disorder association and looks as follows: <br/></div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><pre>Disease title, OMIM id referring to a disease and evidence code| gene symbol and synonyms| OMIM id <del class="diffchange diffchange-inline">reffering </del>to gene entry| locus </pre><br/></div></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><pre>Disease title, OMIM id referring to a disease and evidence code| gene symbol and synonyms| OMIM id <ins class="diffchange diffchange-inline">referring </ins>to gene entry| locus </pre><br/></div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The evidence code is a number in parentheses and indicates whether the evidence for association (mutation) was positioned by mapping the wild type gene (1), by mapping the disease phenotype itself (2), or by both approaches (3). The last "3", includes mapping of the wild type gene combined with demonstration of a mutation in that gene in association with the disorder. To ensure the best possible data for our research, <del class="diffchange diffchange-inline">I </del>used only entries denoted with (3).</div></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>The evidence code is a number in parentheses and indicates whether the evidence for association (mutation) was positioned by mapping the wild type gene (1), by mapping the disease phenotype itself (2), or by both approaches (3). The last "3", includes mapping of the wild type gene combined with demonstration of a mutation in that gene in association with the disorder. To ensure the best possible data for our research, <ins class="diffchange diffchange-inline">we </ins>used only entries denoted with (3).</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;"></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;"></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>===Example of Morbid Map entry:===</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>===Example of Morbid Map entry:===</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l17" >Line 17:</td>
<td colspan="2" class="diff-lineno">Line 17:</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;"></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;"></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>==Pre-processing the Morbid Map==</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>==Pre-processing the Morbid Map==</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>For the map to be readily cross-referenced with our system, <del class="diffchange diffchange-inline">I translated the </del>gene symbols into <del class="diffchange diffchange-inline">the </del>Entrez Gene Identifiers. Great care was taken translating gene names into Gene identifiers because the names are not unique. <del class="diffchange diffchange-inline">I used </del>taxonomy (human) and chromosome limits (locus info is present in Morbid Map) <del class="diffchange diffchange-inline">and searched </del>gene symbol name first in the <del class="diffchange diffchange-inline">geneinfo </del>table released by the <del class="diffchange diffchange-inline">Gene </del>database<del class="diffchange diffchange-inline">, in case of </del>no hit, <del class="diffchange diffchange-inline">I broadened </del>the search <del class="diffchange diffchange-inline">and looked at </del>synonyms and locus names. Despite this effort, there were about 140 unresolved cases (no hit or too many hits) in the Morbid Map.</div></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>For the map to be readily cross-referenced with our system, gene symbols <ins class="diffchange diffchange-inline">were translated </ins>into <ins class="diffchange diffchange-inline">their corresponding </ins>Entrez Gene Identifiers. Great care was taken translating gene names into Gene identifiers because the names are not unique. <ins class="diffchange diffchange-inline">The </ins>taxonomy <ins class="diffchange diffchange-inline">identifier 9606 </ins>(human) and chromosome limits (locus info is present in Morbid Map) <ins class="diffchange diffchange-inline">were used to limit search results for the </ins>gene symbol name first in the <ins class="diffchange diffchange-inline">gene info </ins>table <ins class="diffchange diffchange-inline">(</ins>released by the <ins class="diffchange diffchange-inline">EntrezGene </ins>database<ins class="diffchange diffchange-inline">). In those cases where </ins>no hit <ins class="diffchange diffchange-inline">was found</ins>, the search <ins class="diffchange diffchange-inline">was broadened to include </ins>synonyms and locus names <ins class="diffchange diffchange-inline">for the gene name listed in Morbid Map</ins>. Despite this effort, there were about 140 unresolved cases (no hit or too many hits) in the Morbid Map.</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">I also parsed out </del>evidence code and disease OMIM id from the disease title into separate database fields. There are nearly 800 entries with no disease omim id specified. These are mostly distinct titles.</div></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 class="diffchange diffchange-inline">The </ins>evidence code and disease OMIM id <ins class="diffchange diffchange-inline">were separated </ins>from the disease title <ins class="diffchange diffchange-inline">column </ins>into separate database fields. There are nearly 800 entries with no disease omim id specified. These are mostly distinct titles.</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;"></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;"></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;"></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;"></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>==Matching Morbid map entries==</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>==Matching Morbid map entries==</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In many cases, one disease appears in Morbid Map in association with more than one gene. These “multigenic” diseases are the most valuable to <del class="diffchange diffchange-inline">me </del>since <del class="diffchange diffchange-inline">I </del>can study the properties of the sub-networks that these genes form within the <del class="diffchange diffchange-inline">large </del>human network. <del class="diffchange diffchange-inline">It is</del>, <del class="diffchange diffchange-inline">therefore, necessary to group </del>the disease <del class="diffchange diffchange-inline">titles together</del>. However, <del class="diffchange diffchange-inline">the </del>titles <del class="diffchange diffchange-inline">are </del>not always exactly the same and <del class="diffchange diffchange-inline">vary </del>in detail. These variations often describe disease sub-types or are a result of a simple inconsistency.</div></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>In many cases, one disease appears in Morbid Map in association with more than one gene. These “multigenic” diseases are the most valuable to <ins class="diffchange diffchange-inline">us </ins>since <ins class="diffchange diffchange-inline">we </ins>can study the properties of the sub-networks that these genes form within the <ins class="diffchange diffchange-inline">larger </ins>human network. <ins class="diffchange diffchange-inline">Groups of disease-gene association were constructed using disease titles (first column in the Morbid Map). In some cases</ins>, <ins class="diffchange diffchange-inline">multiple entries have identical titles; these were assigned </ins>the <ins class="diffchange diffchange-inline">same </ins>disease <ins class="diffchange diffchange-inline">group identifier</ins>. However, titles <ins class="diffchange diffchange-inline">were </ins>not always exactly the same and <ins class="diffchange diffchange-inline">varied </ins>in <ins class="diffchange diffchange-inline">the </ins>detail <ins class="diffchange diffchange-inline">given</ins>. These variations often describe disease sub-types or are a result of a simple inconsistency.</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;"></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;"></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>===Example of a disease with sub-types:===</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>===Example of a disease with sub-types:===</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l53" >Line 53:</td>
<td colspan="2" class="diff-lineno">Line 53:</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;"></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;"></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>==Grouping of titles in morbid map==</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>==Grouping of titles in morbid map==</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Using simple text parsing rules, titles in morbid map <del class="diffchange diffchange-inline">are </del>grouped using <del class="diffchange diffchange-inline">string matching technique</del>. Highly similar or identical titles are pooled into one group of disorders. To initiate the text search, the titles are stripped of everything behind the first comma (if there is no comma, disease tag, omim id are taken off) or after keywords “due to” or “with” that tend to specify subtypes of a main phenotype. Before the search for matching titles, white spaces, stand-alone digits and roman numerals are also removed. The resulting search strings are anchored at the beginning to select for partial title hits. Two kinds of opening brackets (“{”,”[”) are allowed to occur at the begininng, these brackets are used by OMIM as a special symbol to indicate susceptibility to certain conditions.</div></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>Using simple text parsing rules, titles in morbid map <ins class="diffchange diffchange-inline">were </ins>grouped using <ins class="diffchange diffchange-inline">regular expression methods</ins>. Highly similar or identical titles are pooled into one group of disorders. To initiate the text search, the titles are stripped of everything behind the first comma (if there is no comma, disease tag, omim id are taken off) or after keywords “due to” or “with” that tend to specify subtypes of a main phenotype. Before the search for matching titles, white spaces, stand-alone digits and roman numerals are also removed. The resulting search strings are anchored at the beginning to select for partial title hits. Two kinds of opening brackets (“{”,”[”) are allowed to occur at the begininng, these brackets are used by OMIM as a special symbol to indicate susceptibility to certain conditions.</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">The </del>sql regular expression search <del class="diffchange diffchange-inline">is </del>used to form an initial group of hits. Every partial hit <del class="diffchange diffchange-inline">is </del>examined. To be accepted, the match <del class="diffchange diffchange-inline">has </del>to either end at the word boundary or with punctuation (“,”,”-”,”/”,”(”) or to continue with allowed suffixes (presently “s”, “tous”, “tosis” to accommodate <del class="diffchange diffchange-inline">match </del>of, for example, adenomatous and adenomatosis). Testing for word boundaries is necessary to exclude false matches that result from partial word matching (e.g. AICA versus Aicardi, POR versus Porencephaly).</div></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 class="diffchange diffchange-inline">A </ins>sql regular expression search <ins class="diffchange diffchange-inline">was </ins>used to form an initial group of hits. Every partial hit <ins class="diffchange diffchange-inline">was </ins>examined. To be accepted, the match <ins class="diffchange diffchange-inline">had </ins>to either end at the word boundary or with punctuation (“,”,”-”,”/”,”(”) or to continue with allowed suffixes (presently “s”, “tous”, “tosis” to accommodate <ins class="diffchange diffchange-inline">matches </ins>of, for example, adenomatous and adenomatosis). Testing for word boundaries is necessary to exclude false matches that result from partial word matching (e.g. AICA versus Aicardi, POR versus Porencephaly).</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>All approved matches <del class="diffchange diffchange-inline">are </del>assigned the same integer disease identifier. The Morbid Map released in August 2008 contained 3700 entries with disease tag “(3)” and <del class="diffchange diffchange-inline">that </del>were assigned to 1500 disease groups.</div></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>All approved matches <ins class="diffchange diffchange-inline">were </ins>assigned the same integer disease identifier. The Morbid Map released in August 2008 contained 3700 entries with disease tag “(3)” and <ins class="diffchange diffchange-inline">these </ins>were assigned to 1500 disease groups<ins class="diffchange diffchange-inline">. This mapping of disease genes into groups is referred to as DiG</ins>.</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;"></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;"></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>==Testing disease groups==</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>==Testing disease groups==</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">Publication </del>from Goh et al. <del class="diffchange diffchange-inline">presents </del>a similar effort in processing the Morbid Map. The release from December 2005 was processed by string matching to fuse sub-types of diseases. The original 2929 entries with disease tag “(3)” were grouped into 1284 groups and manually classified to 22 classes pointing to a physiological system affected in human body. <del class="diffchange diffchange-inline">I </del>used <del class="diffchange diffchange-inline">this publication </del>to assess the accuracy of <del class="diffchange diffchange-inline">my own </del>disease grouping.</div></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 class="diffchange diffchange-inline">The publication </ins>from Goh et al. <ins class="diffchange diffchange-inline">[[#ref1|[1]]] presented </ins>a similar effort in processing the Morbid Map. The <ins class="diffchange diffchange-inline">Morbid Map </ins>release from December 2005 was processed by string matching to fuse sub-types of diseases. The original 2929 entries with disease tag “(3)” were grouped into 1284 groups and manually classified to 22 classes pointing to a physiological system affected in <ins class="diffchange diffchange-inline">the </ins>human body. <ins class="diffchange diffchange-inline">This publication was </ins>used to assess the accuracy of <ins class="diffchange diffchange-inline">our </ins>disease grouping.</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">I transferred the </del>grouping of Goh et al. <del class="diffchange diffchange-inline">into </del>August 2008 Morbid Map<del class="diffchange diffchange-inline">, this effort </del>left about 400 newer entries unmatched. The groupings for the rest of the entries were compared. In about 100 cases, <del class="diffchange diffchange-inline">my </del>divisions were too conservative and groups needed to be fused. <del class="diffchange diffchange-inline">The </del>titles <del class="diffchange diffchange-inline">are sometimes </del>not consistent in the Morbid Map, the word order <del class="diffchange diffchange-inline">sometimes does </del>not match or the most relevant word <del class="diffchange diffchange-inline">is </del>not <del class="diffchange diffchange-inline">placed </del>at the beginning. Also, cancer names <del class="diffchange diffchange-inline">vary </del>a lot. Most likely, Goh et al. manually intervened to sort out such groups. To deal with these inconsistent titles, <del class="diffchange diffchange-inline">I created </del>new titles that <del class="diffchange diffchange-inline">can </del>be processed correctly by the title matching parser and added <del class="diffchange diffchange-inline">these </del>to the <del class="diffchange diffchange-inline">database </del>table <del class="diffchange diffchange-inline">that facilitates the </del>title matching. These new titles <del class="diffchange diffchange-inline">are </del>often just <del class="diffchange diffchange-inline">variation </del>on the original one, with a different word order or an extra comma. The changes to the titles <del class="diffchange diffchange-inline">are </del>generated by a sql script and can be used on a new version of the Morbid Map to re-create the groups. The first version of this script contains about 150 sql statements.</div></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 class="diffchange diffchange-inline">The disease </ins>grouping of Goh et al. <ins class="diffchange diffchange-inline">[[#ref1|[1]]] was transferred onto the </ins>August 2008 Morbid Map<ins class="diffchange diffchange-inline">. This </ins>left about 400 newer entries unmatched. The groupings for the rest of the entries were compared <ins class="diffchange diffchange-inline">(i.e. the genes that were mapped by both the Goh study and in our DiG list)</ins>. In about 100 cases, <ins class="diffchange diffchange-inline">DiG </ins>divisions were too conservative and groups needed to be fused. <ins class="diffchange diffchange-inline">Sometimes the </ins>titles <ins class="diffchange diffchange-inline">were </ins>not consistent <ins class="diffchange diffchange-inline">between different entries </ins>in the Morbid Map<ins class="diffchange diffchange-inline">. Inother cases</ins>, the word order <ins class="diffchange diffchange-inline">did </ins>not match or the most relevant word <ins class="diffchange diffchange-inline">did </ins>not <ins class="diffchange diffchange-inline">occur </ins>at the beginning <ins class="diffchange diffchange-inline">of the title</ins>. Also, cancer names <ins class="diffchange diffchange-inline">varied </ins>a lot. Most likely, Goh et al. manually intervened to sort out such groups. To deal with these inconsistent titles, new titles <ins class="diffchange diffchange-inline">were created </ins>that <ins class="diffchange diffchange-inline">could </ins>be processed correctly by the title matching parser and <ins class="diffchange diffchange-inline">these to were </ins>added to the table <ins class="diffchange diffchange-inline">prior to </ins>title matching. These new titles <ins class="diffchange diffchange-inline">were </ins>often just <ins class="diffchange diffchange-inline">variations </ins>on the original one, with a different word order or an extra comma. The changes to the titles <ins class="diffchange diffchange-inline">were </ins>generated by a sql script and can be used on a new version of the Morbid Map to re-create the groups. The first version of this script contains about 150 sql statements.</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The total numbers of groups is about 1500. <del class="diffchange diffchange-inline">At </del>the end, about 25 groups were deliberately kept more conservative than Goh et al.; i.e. one group by Goh et al. corresponds to two or more <del class="diffchange diffchange-inline">of </del>disease groups. In 25 cases, <del class="diffchange diffchange-inline">I </del>fused <del class="diffchange diffchange-inline">groups </del>that are separated in Goh et al. Overall, thorough manual checks were done ONLY on groups that were different <del class="diffchange diffchange-inline">in </del>Goh et al.</div></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>The total numbers of groups is about 1500. <ins class="diffchange diffchange-inline">In </ins>the end, about 25 groups were deliberately kept more conservative than Goh et al.; i.e. one group by Goh et al. corresponds to two or more disease groups <ins class="diffchange diffchange-inline">in DiG</ins>. In 25 cases, <ins class="diffchange diffchange-inline">groups were </ins>fused that are separated in Goh et al. Overall, thorough manual checks were done <ins class="diffchange diffchange-inline">'''</ins>ONLY<ins class="diffchange diffchange-inline">''' </ins>on groups that were different <ins class="diffchange diffchange-inline">between </ins>Goh et al<ins class="diffchange diffchange-inline">. and DiG</ins>.</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;"></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;"></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>==Multigenic groups of diseases==</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>==Multigenic groups of diseases==</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l69" >Line 69:</td>
<td colspan="2" class="diff-lineno">Line 69:</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;"></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;"></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>==Reference==</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>==Reference==</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL, The human disease network. Proc Natl Acad Sci USA. 2007 May 22;104(21):8685-90</div></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 class="diffchange diffchange-inline"><div id="ref1">1. </ins>Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL, The human disease network. Proc Natl Acad Sci USA. 2007 May 22;104(21):8685-90 <ins class="diffchange diffchange-inline">PMID 17502601</ins></div></td></tr>
</table>Ian.donaldsonhttp://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=943&oldid=prevKaterim: /* OMIM Morbid map */2009-04-04T06:52:18Z<p><span dir="auto"><span class="autocomment">OMIM Morbid map</span></span></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 06:52, 4 April 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l8" >Line 8:</td>
<td colspan="2" class="diff-lineno">Line 8:</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;"></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;"></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>==OMIM Morbid map==</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>==OMIM Morbid map==</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The largest and the most reliable disease association list is available from the Online Mendelian Inheritance in Man [http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim (OMIM) database]. The Morbid Map maintained within this resource lists gene and disease associations and is exported as simple table with about 5000 entries. Each line in this table corresponds to one gene – disorder association and looks as follows: <br/></div></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>The largest and the most reliable disease association list is available from the Online Mendelian Inheritance in Man [http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim (OMIM) database]. The Morbid Map<ins class="diffchange diffchange-inline">, </ins>maintained within this resource<ins class="diffchange diffchange-inline">, </ins>lists gene and disease associations and is exported as simple table with about 5000 entries. Each line in this table corresponds to one gene – disorder association and looks as follows: <br/></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><pre>Disease title, OMIM id referring to a disease and evidence code| gene symbol and synonyms| OMIM id reffering to gene entry| locus </pre><br/></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><pre>Disease title, OMIM id referring to a disease and evidence code| gene symbol and synonyms| OMIM id reffering to gene entry| locus </pre><br/></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>The evidence code is a number in parentheses and indicates whether the evidence for association (mutation) was positioned by mapping the wild type gene (1), by mapping the disease phenotype itself (2), or by both approaches (3). The last "3", includes mapping of the wild type gene combined with demonstration of a mutation in that gene in association with the disorder. To ensure the best possible data for our research, I used only entries denoted with (3).</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>The evidence code is a number in parentheses and indicates whether the evidence for association (mutation) was positioned by mapping the wild type gene (1), by mapping the disease phenotype itself (2), or by both approaches (3). The last "3", includes mapping of the wild type gene combined with demonstration of a mutation in that gene in association with the disorder. To ensure the best possible data for our research, I used only entries denoted with (3).</div></td></tr>
</table>Katerimhttp://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=942&oldid=prevKaterim: /* OMIM Morbid map */2009-04-04T06:47:42Z<p><span dir="auto"><span class="autocomment">OMIM Morbid map</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<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 06:47, 4 April 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l8" >Line 8:</td>
<td colspan="2" class="diff-lineno">Line 8:</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;"></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;"></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>==OMIM Morbid map==</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>==OMIM Morbid map==</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The largest and the most reliable disease association list is available from the Online Mendelian Inheritance in Man <del class="diffchange diffchange-inline">(OMIM) database </del>[http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim <del class="diffchange diffchange-inline">omim</del>]. The Morbid Map maintained within this resource lists gene and disease associations and is exported as simple table with about 5000 entries. Each line in this table corresponds to one gene – disorder association and looks as follows: <br/></div></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>The largest and the most reliable disease association list is available from the Online Mendelian Inheritance in Man [http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim <ins class="diffchange diffchange-inline">(OMIM) database</ins>]. The Morbid Map maintained within this resource lists gene and disease associations and is exported as simple table with about 5000 entries. Each line in this table corresponds to one gene – disorder association and looks as follows: <br/></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><pre>Disease title, OMIM id referring to a disease and evidence code| gene symbol and synonyms| OMIM id reffering to gene entry| locus </pre><br/></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><pre>Disease title, OMIM id referring to a disease and evidence code| gene symbol and synonyms| OMIM id reffering to gene entry| locus </pre><br/></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>The evidence code is a number in parentheses and indicates whether the evidence for association (mutation) was positioned by mapping the wild type gene (1), by mapping the disease phenotype itself (2), or by both approaches (3). The last "3", includes mapping of the wild type gene combined with demonstration of a mutation in that gene in association with the disorder. To ensure the best possible data for our research, I used only entries denoted with (3).</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>The evidence code is a number in parentheses and indicates whether the evidence for association (mutation) was positioned by mapping the wild type gene (1), by mapping the disease phenotype itself (2), or by both approaches (3). The last "3", includes mapping of the wild type gene combined with demonstration of a mutation in that gene in association with the disorder. To ensure the best possible data for our research, I used only entries denoted with (3).</div></td></tr>
</table>Katerimhttp://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=941&oldid=prevKaterim: /* Introduction */2009-04-04T06:46:08Z<p><span dir="auto"><span class="autocomment">Introduction</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<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 06:46, 4 April 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2" >Line 2:</td>
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<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;"></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;"></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>==Introduction==</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>==Introduction==</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>We investigate properties of human disease genes within the protein-protein interaction network. Two essential datasets required for this research <del class="diffchange diffchange-inline">are</del>:</div></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>We investigate properties of human disease genes within the protein-protein interaction network. Two essential datasets <ins class="diffchange diffchange-inline">are </ins>required for this research:</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>#human protein-protein interaction network</div></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 class="diffchange diffchange-inline">the </ins>human protein-protein interaction network <ins class="diffchange diffchange-inline">and</ins></div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>#list of genes associated with genetic disorders</div></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 class="diffchange diffchange-inline">a </ins>list of genes associated with genetic disorders</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The human interaction network is taken from the <del class="diffchange diffchange-inline">iRefIndex </del>[http://irefindex.uio.no <del class="diffchange diffchange-inline">irefindex</del>] resource and the creation of the disease gene list is described <del class="diffchange diffchange-inline">in </del>this page.</div></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>The human interaction network is taken from the [http://irefindex.uio.no <ins class="diffchange diffchange-inline">iRefIndex</ins>] resource and the creation of the disease gene list is described <ins class="diffchange diffchange-inline">on </ins>this page.</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2"> </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;"></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;"></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>==OMIM Morbid map==</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>==OMIM Morbid map==</div></td></tr>
</table>Katerimhttp://irefindex.vib.be/wiki/index.php?title=DiG:_Disease_groups&diff=940&oldid=prevKaterim: /* Example of Morbid Map entry: */2009-04-04T06:35:43Z<p><span dir="auto"><span class="autocomment">Example of Morbid Map entry:</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<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 06:35, 4 April 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l14" >Line 14:</td>
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<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;"></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;"></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>===Example of Morbid Map entry:===</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>===Example of Morbid Map entry:===</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"><tt>Parkinson disease, 168600 (3) |TBP, SCA17|600075|6q27</tt></del></div></td><td colspan="2"> </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;"></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;"></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;"><pre>Parkinson disease, 168600 (3) |TBP, SCA17|600075|6q27</pre></ins></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;"></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;"></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>==Pre-processing the Morbid Map==</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>==Pre-processing the Morbid Map==</div></td></tr>
</table>Katerim