https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&feed=atom&action=historyAnnotation Conf. Call, April 28, 2015 - Revision history2024-03-29T09:25:31ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=58079&oldid=prevKchris: /* Discussion */2015-08-21T16:32:27Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The 'NLS bearing...' annotation is wrong- it is for proteins that can bind to NLS signals and import them into the nucleus</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The 'NLS bearing...' annotation is wrong- it is for proteins that can bind to NLS signals and import them into the nucleus</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Chromatin- is not just histones and DNA. Should Txn factors be annotated to chromatin? Would you make a CC annotation to chromatin over a MF annotation to chromatin binding when you have ChiP evidence? Karen mentioned that <del style="font-weight: bold; text-decoration: none;">in the paper </del>she <del style="font-weight: bold; text-decoration: none;">worked on </del>with the <del style="font-weight: bold; text-decoration: none;">Norway folks they decided all ChiP experiments should be </del>CC. David mentioned that the way he decides between the two is : When you are binding chromatin you are not part of the chromatin. Is txn factor part of chromatin? We need to resolve this issue at the next GOC meeting (Midori has some rules, so does David). We will collect some use cases and present it at the GOC meeting. What should be included in the definition of chromatin? Note that we also have terms like 'transcriptionally active chromatin' and 'transcriptionally silent chromatin'.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Chromatin- is not just histones and DNA. Should Txn factors be annotated to chromatin? Would you make a CC annotation to chromatin over a MF annotation to chromatin binding when you have ChiP evidence? Karen mentioned that <ins style="font-weight: bold; text-decoration: none;">that </ins>she <ins style="font-weight: bold; text-decoration: none;">has generally used "colocalized </ins>with<ins style="font-weight: bold; text-decoration: none;">" </ins>the CC <ins style="font-weight: bold; text-decoration: none;">term "chromatin"</ins>. David mentioned that the way he decides between the two is : When you are binding chromatin you are not part of the chromatin. Is txn factor part of chromatin? We need to resolve this issue at the next GOC meeting (Midori has some rules, so does David). We will collect some use cases and present it at the GOC meeting. What should be included in the definition of chromatin? Note that we also have terms like 'transcriptionally active chromatin' and 'transcriptionally silent chromatin'.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**DNA</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**DNA</div></td></tr>
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</table>Kchrishttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=57012&oldid=prevVanaukenk: /* Discussion */2015-05-12T18:44:32Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The 'NLS bearing...' annotation is wrong- it is for proteins that can bind to NLS signals and import them into the nucleus</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The 'NLS bearing...' annotation is wrong- it is for proteins that can bind to NLS signals and import them into the nucleus</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Chromatin- is not just histones and DNA. Should Txn factors be annotated to chromatin? Would you make a CC annotation to chromatin over a MF annotation to chromatin binding when you have ChiP evidence? Karen mentioned that in the paper she worked on with the Norway folks they decided all ChiP experiments should be CC. David mentioned that the way he decides between the two is : When you are binding chromatin you are not part of the chromatin. Is txn factor part of chromatin? We need to resolve this issue at the next GOC meeting (Midori has some rules, so does David). We will collect some use cases and present it at the GOC meeting. What should be included in the definition of chromatin? </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Chromatin- is not just histones and DNA. Should Txn factors be annotated to chromatin? Would you make a CC annotation to chromatin over a MF annotation to chromatin binding when you have ChiP evidence? Karen mentioned that in the paper she worked on with the Norway folks they decided all ChiP experiments should be CC. David mentioned that the way he decides between the two is : When you are binding chromatin you are not part of the chromatin. Is txn factor part of chromatin? We need to resolve this issue at the next GOC meeting (Midori has some rules, so does David). We will collect some use cases and present it at the GOC meeting. What should be included in the definition of chromatin? <ins style="font-weight: bold; text-decoration: none;">Note that we also have terms like 'transcriptionally active chromatin' and 'transcriptionally silent chromatin'.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**DNA</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**DNA</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**RNA</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**RNA</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=57011&oldid=prevVanaukenk: /* Discussion */2015-05-12T18:42:10Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histones</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histones</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**histone modifying complexes?</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**histone modifying complexes? <ins style="font-weight: bold; text-decoration: none;">- these are not children of chromatin in the CC</ins></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**chromtin re-modeling complexes?</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**chromtin re-modeling complexes? <ins style="font-weight: bold; text-decoration: none;">- these are also not children of chromatin in the CC</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**transcription factors?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**transcription factors?</div></td></tr>
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</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=57010&oldid=prevVanaukenk: /* Discussion */2015-05-12T18:39:06Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histones</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histones</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histone modifying complexes?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histone modifying complexes?</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**re-modeling complexes?</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**<ins style="font-weight: bold; text-decoration: none;">chromtin </ins>re-modeling complexes?</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**transcription factors?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**transcription factors?</div></td></tr>
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</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=57009&oldid=prevVanaukenk: /* Discussion */2015-05-12T18:38:14Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histones</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histones</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**histone modifying <del style="font-weight: bold; text-decoration: none;">enzymes and associated </del>complexes?</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**histone modifying <ins style="font-weight: bold; text-decoration: none;">complexes?</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**re-modeling </ins>complexes?</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**transcription factors?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**transcription factors?</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=57008&oldid=prevVanaukenk: /* Discussion */2015-05-12T18:35:30Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The 'NLS bearing...' annotation is wrong- it is for proteins that can bind to NLS signals and import them into the nucleus</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The 'NLS bearing...' annotation is wrong- it is for proteins that can bind to NLS signals and import them into the nucleus</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Chromatin- is not just histones and DNA. Should Txn factors be annotated to chromatin? Would you make a CC annotation to chromatin over a MF annotation to chromatin binding when you have ChiP evidence? Karen mentioned that in the paper she worked on with the Norway folks they decided all ChiP experiments should be CC. David mentioned that the way he decides between the two is : When you are binding chromatin you are not part of the chromatin. Is txn factor part of chromatin? We need to resolve this issue at the next GOC meeting (Midori has some rules, so does David). We will collect some use cases and present it at the GOC meeting</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Chromatin- is not just histones and DNA. Should Txn factors be annotated to chromatin? Would you make a CC annotation to chromatin over a MF annotation to chromatin binding when you have ChiP evidence? Karen mentioned that in the paper she worked on with the Norway folks they decided all ChiP experiments should be CC. David mentioned that the way he decides between the two is : When you are binding chromatin you are not part of the chromatin. Is txn factor part of chromatin? We need to resolve this issue at the next GOC meeting (Midori has some rules, so does David). We will collect some use cases and present it at the GOC meeting<ins style="font-weight: bold; text-decoration: none;">. What should be included in the definition of chromatin? </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**DNA</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**DNA</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**RNA</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**RNA</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histones</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**histones</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**histone modifying enzymes and associated complexes</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**histone modifying enzymes and associated complexes<ins style="font-weight: bold; text-decoration: none;">?</ins></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**transcription factors</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**transcription factors<ins style="font-weight: bold; text-decoration: none;">?</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* RNA pol II binding- this is redundant with RNA Pol II txn factor complex annotation. Is there a link between the two? This is not always true, so no.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* RNA pol II binding- this is redundant with RNA Pol II txn factor complex annotation. Is there a link between the two? This is not always true, so no.</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=57007&oldid=prevVanaukenk: /* Discussion */2015-05-12T18:34:39Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:34, 12 May 2015</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The 'NLS bearing...' annotation is wrong- it is for proteins that can bind to NLS signals and import them into the nucleus</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The 'NLS bearing...' annotation is wrong- it is for proteins that can bind to NLS signals and import them into the nucleus</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Chromatin- is not just histones and DNA. Should Txn factors be annotated to chromatin? Would you make a CC annotation to chromatin over a MF annotation to chromatin binding when you have ChiP evidence? Karen mentioned that in the paper she worked on with the Norway folks they decided all ChiP experiments should be CC. David mentioned that the way he decides between the two is : When you are binding chromatin you are not part of the chromatin. Is txn factor part of chromatin? We need to resolve this issue at the next GOC meeting (Midori has some rules, so does David). We will collect some use cases and present it at the GOC meeting</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Chromatin- is not just histones and DNA. Should Txn factors be annotated to chromatin? Would you make a CC annotation to chromatin over a MF annotation to chromatin binding when you have ChiP evidence? Karen mentioned that in the paper she worked on with the Norway folks they decided all ChiP experiments should be CC. David mentioned that the way he decides between the two is : When you are binding chromatin you are not part of the chromatin. Is txn factor part of chromatin? We need to resolve this issue at the next GOC meeting (Midori has some rules, so does David). We will collect some use cases and present it at the GOC meeting</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**DNA</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**RNA</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**histones</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**histone modifying enzymes and associated complexes</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**transcription factors</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* RNA pol II binding- this is redundant with RNA Pol II txn factor complex annotation. Is there a link between the two? This is not always true, so no.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* RNA pol II binding- this is redundant with RNA Pol II txn factor complex annotation. Is there a link between the two? This is not always true, so no.</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=56998&oldid=prevVanaukenk: /* Discussion */2015-05-11T16:40:16Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:40, 11 May 2015</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* '''Cystin annotation to GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity''' Both cystin and necdin are able to activate transcription from the Myc P1 promoter above basal levels in vitro (see Figure 6C), although necdin activates to a greater degree than cystin. However, when cystin and necdin are expressed together, there is an antagonist effect on Myc transcription: Myc P1 promoter activity is lower than with necdin alone. The mechanism for this regulation is not demonstrated in this experiment; they did not show that cystin is specifically negatively regulating the DNA binding transcription factor activity of necdin. But the definition of '''GO:00043433:''' Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription, implies that it negatively regulates the totality of transcription not just the DNA binding part. So this term, as defined, would be fine to annotate cystin. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* '''Cystin annotation to GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity''' Both cystin and necdin are able to activate transcription from the Myc P1 promoter above basal levels in vitro (see Figure 6C), although necdin activates to a greater degree than cystin. However, when cystin and necdin are expressed together, there is an antagonist effect on Myc transcription: Myc P1 promoter activity is lower than with necdin alone. The mechanism for this regulation is not demonstrated in this experiment; they did not show that cystin is specifically negatively regulating the DNA binding transcription factor activity of necdin. But the definition of '''GO:00043433:''' Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription, implies that it negatively regulates the totality of transcription not just the DNA binding part. So this term, as defined, would be fine to annotate cystin. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Is cystin regulating necdin? There is no evidence to show that cystin is regulating necdin - '''What would constitute evidence for this? The paper does show physical interaction between the two proteins and an effect on activity when co-transfected.''' So we can't put necdin as the regulation target of cystin. How would you capture the fact that cystin has the antagonist effect when necdin is present but it has the opposite role when it is acting alone? Would you use the evidence code or Col-16?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Is cystin regulating necdin? There is no evidence to show that cystin is regulating necdin - '''What would constitute evidence for this? The paper does show physical interaction between the two proteins and an effect on activity when co-transfected.''' So we can't put necdin as the regulation target of cystin. How would you capture the fact that cystin has the antagonist effect when necdin is present but it has the opposite role when it is acting alone? Would you use the evidence code or Col-16?</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Would you use IGI as the evidence for how cystin interacts with necdin? Is cotransfection considered IGI? Both Rama and Midori thought this was not IGI based on current definition. Ruth, Rebecca and Rachael felt this would be IGI. Kimberly - I had originally used the IDA evidence code for the co-transfection experiment, but it seems that what we are really trying to capture with annotating this experiment is a functional interaction between two gene products. Although the type of experiment differs from traditional genetic experiments using multiply mutant strains, the conclusion is similar: these gene products functionally interact, even if we don't know the exact mechanism. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Would you use IGI as the evidence for how cystin interacts with necdin? Is cotransfection considered IGI? Both Rama and Midori thought this was not IGI based on current definition. Ruth, Rebecca and Rachael felt this would be IGI. Kimberly - I had originally used the IDA evidence code for the co-transfection experiment, but it seems that what we are really trying to capture with annotating this experiment is a functional interaction between two gene products. Although the type of experiment differs from traditional genetic experiments using multiply mutant strains, the conclusion is similar: these gene products functionally interact, even if we don't know the exact mechanism<ins style="font-weight: bold; text-decoration: none;">. The IGI evidence code therefore seems more appropriate to me now</ins>. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason for use of IGI:''''' 2 cDNA constructs (cystin and necdin) transfected into a cell line, the effect is only seen when both constructs are present, therefore the use of IGI code enables the cystin to be annotated to negative reg of transcription (child term), and the addition of the necdin protein ID in the WITH field (the reciprocal annotation would not be created).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason for use of IGI:''''' 2 cDNA constructs (cystin and necdin) transfected into a cell line, the effect is only seen when both constructs are present, therefore the use of IGI code enables the cystin to be annotated to negative reg of transcription (child term), and the addition of the necdin protein ID in the WITH field (the reciprocal annotation would not be created).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason against use of IGI:''''' When only one of these genes is transfected into the cells the annotations created (pos reg of transcription, child term) are supported by the IDA evidence code not the IMP evidence code. The GOC documentation on IGI states: Includes any combination of alterations in the sequence (mutation) or expression of more than one gene/gene product.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason against use of IGI:''''' When only one of these genes is transfected into the cells the annotations created (pos reg of transcription, child term) are supported by the IDA evidence code not the IMP evidence code. The GOC documentation on IGI states: Includes any combination of alterations in the sequence (mutation) or expression of more than one gene/gene product.</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=56997&oldid=prevVanaukenk: /* Discussion */2015-05-11T16:39:18Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* '''Cystin annotation to GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity''' Both cystin and necdin are able to activate transcription from the Myc P1 promoter above basal levels in vitro (see Figure 6C), although necdin activates to a greater degree than cystin. However, when cystin and necdin are expressed together, there is an antagonist effect on Myc transcription: Myc P1 promoter activity is lower than with necdin alone. The mechanism for this regulation is not demonstrated in this experiment; they did not show that cystin is specifically negatively regulating the DNA binding transcription factor activity of necdin. But the definition of '''GO:00043433:''' Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription, implies that it negatively regulates the totality of transcription not just the DNA binding part. So this term, as defined, would be fine to annotate cystin. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* '''Cystin annotation to GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity''' Both cystin and necdin are able to activate transcription from the Myc P1 promoter above basal levels in vitro (see Figure 6C), although necdin activates to a greater degree than cystin. However, when cystin and necdin are expressed together, there is an antagonist effect on Myc transcription: Myc P1 promoter activity is lower than with necdin alone. The mechanism for this regulation is not demonstrated in this experiment; they did not show that cystin is specifically negatively regulating the DNA binding transcription factor activity of necdin. But the definition of '''GO:00043433:''' Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription, implies that it negatively regulates the totality of transcription not just the DNA binding part. So this term, as defined, would be fine to annotate cystin. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Is cystin regulating necdin? There is no evidence to show that cystin is regulating necdin - '''What would constitute evidence for this? The paper does show physical interaction between the two proteins and an effect on activity when co-transfected.''' So we can't put necdin as the regulation target of cystin. How would you capture the fact that cystin has the antagonist effect when necdin is present but it has the opposite role when it is acting alone? Would you use the evidence code or Col-16?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Is cystin regulating necdin? There is no evidence to show that cystin is regulating necdin - '''What would constitute evidence for this? The paper does show physical interaction between the two proteins and an effect on activity when co-transfected.''' So we can't put necdin as the regulation target of cystin. How would you capture the fact that cystin has the antagonist effect when necdin is present but it has the opposite role when it is acting alone? Would you use the evidence code or Col-16?</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Would you use IGI as the evidence for how cystin interacts with necdin? Is cotransfection considered IGI? Both Rama and Midori thought this was not IGI based on current definition. Ruth, Rebecca and Rachael felt this would be IGI. <del style="font-weight: bold; text-decoration: none;">'''What is the purpose of </del>the <del style="font-weight: bold; text-decoration: none;">IGI </del>evidence code<del style="font-weight: bold; text-decoration: none;">? In what other context do we use IGI</del>, <del style="font-weight: bold; text-decoration: none;">and in using </del>it what are we <del style="font-weight: bold; text-decoration: none;">saying about </del>the <del style="font-weight: bold; text-decoration: none;">biology?'''</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Would you use IGI as the evidence for how cystin interacts with necdin? Is cotransfection considered IGI? Both Rama and Midori thought this was not IGI based on current definition. Ruth, Rebecca and Rachael felt this would be IGI. <ins style="font-weight: bold; text-decoration: none;">Kimberly - I had originally used </ins>the <ins style="font-weight: bold; text-decoration: none;">IDA </ins>evidence code <ins style="font-weight: bold; text-decoration: none;">for the co-transfection experiment</ins>, <ins style="font-weight: bold; text-decoration: none;">but </ins>it <ins style="font-weight: bold; text-decoration: none;">seems that </ins>what <ins style="font-weight: bold; text-decoration: none;">we </ins>are <ins style="font-weight: bold; text-decoration: none;">really trying to capture with annotating this experiment is a functional interaction between two gene products. Although the type of experiment differs from traditional genetic experiments using multiply mutant strains, the conclusion is similar: these gene products functionally interact, even if </ins>we <ins style="font-weight: bold; text-decoration: none;">don't know </ins>the <ins style="font-weight: bold; text-decoration: none;">exact mechanism. </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason for use of IGI:''''' 2 cDNA constructs (cystin and necdin) transfected into a cell line, the effect is only seen when both constructs are present, therefore the use of IGI code enables the cystin to be annotated to negative reg of transcription (child term), and the addition of the necdin protein ID in the WITH field (the reciprocal annotation would not be created).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason for use of IGI:''''' 2 cDNA constructs (cystin and necdin) transfected into a cell line, the effect is only seen when both constructs are present, therefore the use of IGI code enables the cystin to be annotated to negative reg of transcription (child term), and the addition of the necdin protein ID in the WITH field (the reciprocal annotation would not be created).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason against use of IGI:''''' When only one of these genes is transfected into the cells the annotations created (pos reg of transcription, child term) are supported by the IDA evidence code not the IMP evidence code. The GOC documentation on IGI states: Includes any combination of alterations in the sequence (mutation) or expression of more than one gene/gene product.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason against use of IGI:''''' When only one of these genes is transfected into the cells the annotations created (pos reg of transcription, child term) are supported by the IDA evidence code not the IMP evidence code. The GOC documentation on IGI states: Includes any combination of alterations in the sequence (mutation) or expression of more than one gene/gene product.</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_April_28,_2015&diff=56996&oldid=prevVanaukenk: /* Discussion */2015-05-11T16:17:25Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:17, 11 May 2015</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* '''Cystin annotation to GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity''' Both cystin and necdin are able to activate transcription from the Myc P1 promoter above basal levels in vitro (see Figure 6C), although necdin activates to a greater degree than cystin. However, when cystin and necdin are expressed together, there is an antagonist effect on Myc transcription: Myc P1 promoter activity is lower than with necdin alone. The mechanism for this regulation is not demonstrated in this experiment; they did not show that cystin is specifically negatively regulating the DNA binding transcription factor activity of necdin. But the definition of '''GO:00043433:''' Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription, implies that it negatively regulates the totality of transcription not just the DNA binding part. So this term, as defined, would be fine to annotate cystin. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* '''Cystin annotation to GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity''' Both cystin and necdin are able to activate transcription from the Myc P1 promoter above basal levels in vitro (see Figure 6C), although necdin activates to a greater degree than cystin. However, when cystin and necdin are expressed together, there is an antagonist effect on Myc transcription: Myc P1 promoter activity is lower than with necdin alone. The mechanism for this regulation is not demonstrated in this experiment; they did not show that cystin is specifically negatively regulating the DNA binding transcription factor activity of necdin. But the definition of '''GO:00043433:''' Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription, implies that it negatively regulates the totality of transcription not just the DNA binding part. So this term, as defined, would be fine to annotate cystin. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Is cystin regulating necdin? There is no evidence to show that cystin is regulating necdin - '''What would constitute evidence for this? The paper does show physical interaction between the two proteins and an effect on activity when co-transfected.''' So we can't put necdin as the regulation target of cystin. How would you capture the fact that cystin has the antagonist effect when necdin is present but it has the opposite role when it is acting alone? Would you use the evidence code or Col-16?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Is cystin regulating necdin? There is no evidence to show that cystin is regulating necdin - '''What would constitute evidence for this? The paper does show physical interaction between the two proteins and an effect on activity when co-transfected.''' So we can't put necdin as the regulation target of cystin. How would you capture the fact that cystin has the antagonist effect when necdin is present but it has the opposite role when it is acting alone? Would you use the evidence code or Col-16?</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Would you use IGI as the evidence for how cystin interacts with necdin? Is cotransfection considered IGI? Both Rama and Midori thought this was not IGI based on current definition. Ruth, Rebecca and Rachael felt this would be IGI. '''What is the purpose of the IGI evidence code? <del style="font-weight: bold; text-decoration: none;"> Is it to adhere to a classical definition of genetics interaction, or to help identify functional interactions? </del>In what other context do we use IGI, and in using it what are we saying about the biology?'''</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Would you use IGI as the evidence for how cystin interacts with necdin? Is cotransfection considered IGI? Both Rama and Midori thought this was not IGI based on current definition. Ruth, Rebecca and Rachael felt this would be IGI. '''What is the purpose of the IGI evidence code? In what other context do we use IGI, and in using it what are we saying about the biology?'''</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason for use of IGI:''''' 2 cDNA constructs (cystin and necdin) transfected into a cell line, the effect is only seen when both constructs are present, therefore the use of IGI code enables the cystin to be annotated to negative reg of transcription (child term), and the addition of the necdin protein ID in the WITH field (the reciprocal annotation would not be created).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason for use of IGI:''''' 2 cDNA constructs (cystin and necdin) transfected into a cell line, the effect is only seen when both constructs are present, therefore the use of IGI code enables the cystin to be annotated to negative reg of transcription (child term), and the addition of the necdin protein ID in the WITH field (the reciprocal annotation would not be created).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason against use of IGI:''''' When only one of these genes is transfected into the cells the annotations created (pos reg of transcription, child term) are supported by the IDA evidence code not the IMP evidence code. The GOC documentation on IGI states: Includes any combination of alterations in the sequence (mutation) or expression of more than one gene/gene product.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**'''''Reason against use of IGI:''''' When only one of these genes is transfected into the cells the annotations created (pos reg of transcription, child term) are supported by the IDA evidence code not the IMP evidence code. The GOC documentation on IGI states: Includes any combination of alterations in the sequence (mutation) or expression of more than one gene/gene product.</div></td></tr>
</table>Vanaukenk