https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-02-09&feed=atom&action=history
Annotation Conf. Call 2016-02-09 - Revision history
2024-03-29T07:28:10Z
Revision history for this page on the wiki
MediaWiki 1.40.0
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-02-09&diff=60061&oldid=prev
Vanaukenk: /* Bluejeans Conference Line */
2016-02-19T18:13:30Z
<p><span dir="auto"><span class="autocomment">Bluejeans Conference Line</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:13, 19 February 2016</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>*Recurring meeting URL: https://bluejeans.com/993661940</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>*Recurring meeting URL: https://bluejeans.com/993661940</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;"></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>==Review New IGI Documentation==</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>==Review New IGI Documentation==</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>*Following on from the 2016-01-12 call where we discussed how to annotate co-transfection experiments, below is a draft of new IGI documentation for curation.</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>*Following on from the 2016-01-12 call where we discussed how to annotate co-transfection experiments, below is a draft of new IGI documentation for curation.</div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-02-09&diff=60013&oldid=prev
Vanaukenk: /* Minutes */
2016-02-12T21:40:38Z
<p><span dir="auto"><span class="autocomment">Minutes</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:40, 12 February 2016</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>*Updated version of IGI documentation for final review</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>*Updated version of IGI documentation for final review</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>**[IGI Documentation]</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;">[</ins>[IGI Documentation<ins style="font-weight: bold; text-decoration: none;">]</ins>]</div></td></tr>
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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>[[Category: Annotation Working Group]]</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>[[Category: Annotation Working Group]]</div></td></tr>
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Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-02-09&diff=60012&oldid=prev
Vanaukenk at 21:40, 12 February 2016
2016-02-12T21:40:13Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:40, 12 February 2016</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>*Updated version of IGI documentation for final review</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>*Updated version of IGI documentation for final review</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;">**[IGI Documentation]</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;"><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>[[Category: Annotation Working Group]]</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>[[Category: Annotation Working Group]]</div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-02-09&diff=60011&oldid=prev
Vanaukenk: /* Minutes */
2016-02-12T21:39:08Z
<p><span dir="auto"><span class="autocomment">Minutes</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:39, 12 February 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l145">Line 145:</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>***Add in section on what is NOT IGI an example of rescuing the phenotype of a mutation in one gene by expressing a wild-type copy of that same gene. These experiments support IMP annotations of the gene to a given biological process.</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>***Add in section on what is NOT IGI an example of rescuing the phenotype of a mutation in one gene by expressing a wild-type copy of that same gene. These experiments support IMP annotations of the gene to a given biological process.</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>***Add species information to functional complementation example to highlight that these two genes are from different species.</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>***Add species information to functional complementation example to highlight that these two genes are from different species.</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;"></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;">*Updated version of IGI documentation for final review</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;"><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>[[Category: Annotation Working Group]]</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>[[Category: Annotation Working Group]]</div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-02-09&diff=60009&oldid=prev
Vanaukenk: /* Minutes */
2016-02-12T17:45:38Z
<p><span dir="auto"><span class="autocomment">Minutes</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:45, 12 February 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l143">Line 143:</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>**Major points to address:</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>**Major points to address:</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>***Clarify functional complementation, rescue, and suppression - these experiments are often various flavors of the same thing: expression of a wild-type copy of one gene alters the phenotypic outcome of a mutation in a different gene. The two genes may or may not be from the same species.</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>***Clarify functional complementation, rescue, and suppression - these experiments are often various flavors of the same thing: expression of a wild-type copy of one gene alters the phenotypic outcome of a mutation in a different gene. The two genes may or may not be from the same species.</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>***Add in section on what is NOT IGI<del style="font-weight: bold; text-decoration: none;">, </del>an example of rescuing the phenotype of a mutation in one gene by expressing a wild-type copy of that same gene. These experiments support IMP annotations of the gene to a given biological process.</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>***Add in section on what is NOT IGI an example of rescuing the phenotype of a mutation in one gene by expressing a wild-type copy of that same gene. These experiments support IMP annotations of the gene to a given biological process.</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>***Add species information to functional complementation example to highlight that these two genes are from different species.</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>***Add species information to functional complementation example to highlight that these two genes are from different species.</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;"><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>[[Category: Annotation Working Group]]</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>[[Category: Annotation Working Group]]</div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-02-09&diff=60008&oldid=prev
Vanaukenk: /* Minutes */
2016-02-12T17:45:10Z
<p><span dir="auto"><span class="autocomment">Minutes</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:45, 12 February 2016</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>=Minutes=</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>=Minutes=</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;">*On call:</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;">**Berkeley: Moni</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;">**dictyBase: Bob, Petra</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;">**EBI: Aleks, Alex, David OS., Melanie</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;">**FlyBase: Giulia, Helen</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;">**MGI: Li</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;">**PomBase: Midori</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;">**RGD: Shur-Jen, Stan</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;">**SGD: Edith, Stacia</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;">**SIB: Pascale</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;">**TAIR: Tanya</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;">**UCL: Rachael, Ruth</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;">**WB: Kimberly</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;">**Zfin: Sabrina</ins></div></td></tr>
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<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;">*Reviewed draft of new IGI documentation</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;">**Major points to address:</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;">***Clarify functional complementation, rescue, and suppression - these experiments are often various flavors of the same thing: expression of a wild-type copy of one gene alters the phenotypic outcome of a mutation in a different gene. The two genes may or may not be from the same species.</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;">***Add in section on what is NOT IGI, an example of rescuing the phenotype of a mutation in one gene by expressing a wild-type copy of that same gene. These experiments support IMP annotations of the gene to a given biological process.</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;">***Add species information to functional complementation example to highlight that these two genes are from different species.</ins></div></td></tr>
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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>[[Category: Annotation Working Group]]</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>[[Category: Annotation Working Group]]</div></td></tr>
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Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-02-09&diff=59990&oldid=prev
Vanaukenk: /* Review New IGI Documentation */
2016-02-09T15:33:18Z
<p><span dir="auto"><span class="autocomment">Review New IGI Documentation</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:33, 9 February 2016</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> signaling growth cone formation. In C. elegans, the activity of the upstream-most kinase in one of the MAPK signaling pathways, </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> signaling growth cone formation. In C. elegans, the activity of the upstream-most kinase in one of the MAPK signaling pathways, </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> DLK-1, is stimulated by Ca2+ influx mediated by the EGL-19 voltage-gated calcium channel. EGL-19’s regulatory role in the </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> DLK-1, is stimulated by Ca2+ influx mediated by the EGL-19 voltage-gated calcium channel. EGL-19’s regulatory role in the </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> MAPK-mediated axon regeneration pathway was determined, in part, through doubly mutant animals containing an egl-19 <del style="font-weight: bold; text-decoration: none;">gain-of-</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> MAPK-mediated axon regeneration pathway was determined, in part, through doubly mutant animals containing an egl-19 <ins style="font-weight: bold; text-decoration: none;">hypermorphic </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> <del style="font-weight: bold; text-decoration: none;">function </del>mutation and a dlk-1 loss-of-function mutation that showed a reduced axon regenerative response when compared to <del style="font-weight: bold; text-decoration: none;"> </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> mutation <ins style="font-weight: bold; text-decoration: none;">that results in occasional action potentials with significantly prolonged plateau phases </ins>and a dlk-1 loss-of-</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> </del>egl-19<del style="font-weight: bold; text-decoration: none;">(gf) </del>alone. </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;"> </ins>function mutation that showed a reduced axon regenerative response when compared to egl-19 alone. </div></td></tr>
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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> EGL-19 positive regulation of MAPK cascade involved in axon regeneration (GO:1904922) PMID:20203177 IGI DLK-1</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> EGL-19 positive regulation of MAPK cascade involved in axon regeneration (GO:1904922) PMID:20203177 IGI DLK-1</div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-02-09&diff=59989&oldid=prev
Vanaukenk: Created page with "=Agenda= ==Bluejeans Conference Line== *Recurring meeting URL: https://bluejeans.com/993661940 ==Review New IGI Documentation== *Following on from the 2016-01-12 call where we..."
2016-02-08T22:21:38Z
<p>Created page with "=Agenda= ==Bluejeans Conference Line== *Recurring meeting URL: https://bluejeans.com/993661940 ==Review New IGI Documentation== *Following on from the 2016-01-12 call where we..."</p>
<p><b>New page</b></p><div>=Agenda=<br />
==Bluejeans Conference Line==<br />
*Recurring meeting URL: https://bluejeans.com/993661940<br />
==Review New IGI Documentation==<br />
*Following on from the 2016-01-12 call where we discussed how to annotate co-transfection experiments, below is a draft of new IGI documentation for curation.<br />
*For this call, I'd like to review the new documentation, and solicit input for examples.<br />
*For reference, here is the link to the existing documentation on the web site: http://geneontology.org/page/igi-inferred-genetic-interaction<br />
*Also, please see Ruth's github ticket on the existing IGI documentation: https://github.com/geneontology/go-annotation/issues/1327<br />
IGI: Inferred from Genetic Interaction<br />
<br />
• Genetic interactions such as suppression, enhancement, synergistic (synthetic) interaction, etc.<br />
• Co-transfection experiments in which more than one gene is expressed in a heterologous system to assess functional interaction<br />
• Functional complementation in which a gene from one species is used to complement a mutation in a different species<br />
• Rescue experiments in which expression of one gene rescues the phenotype of a mutation in another gene<br />
• Inference about one gene drawn from the phenotype of a mutation in a different gene??<br />
<br />
The IGI evidence code is used for annotations based on experiments reporting the effects of perturbations in the sequence or <br />
expression of one or more genes or gene products. IGI is also used for experiments that interrogate functional interactions <br />
between two or more genes or gene products when co-expressed, for example, in a cell line. Additional uses of IGI include <br />
functional complementation experiments, phenotypic rescue, and inferences made about one gene drawn from the phenotype of mutations <br />
in a different gene (?). <br />
<br />
Key to deciding whether or not to use the IGI or IMP (Inferred from Mutant Phenotype) evidence code is consideration of the point<br />
of reference (i.e., what is being compared) to determine a possible interaction. If experiments interrogate the effects of <br />
multiple mutations or differences from the control, then use IGI. If experiments interrogate the effects of a single mutation or <br />
difference from the control, then use IMP.<br />
<br />
The IGI evidence code requires curators enter a stable database identifier for the interacting entity in the With/From field of the <br />
Gene Association File (GAF). Independent interactors may be captured in the With/From field by separating each entry with a pipe. <br />
If the interaction experiment involves multiple perturbations simultaneously, e.g. triply mutant strains, then the respective <br />
interactors are separated with a comma.<br />
<br />
'''Genetic interactions such as suppression, enhancement, synergistic (synthetic) interactions, etc.'''<br />
This use of the IGI evidence code refers to the more “traditional” genetic interaction experiments performed in model organisms, <br />
such as ''Saccharomyces cerevisiae'', as well as more recent approaches adopted in a number of different systems such as <br />
RNA-mediated knockdown or genome editing techniques. Note that genetic interaction experiments may be performed with both loss- <br />
and gain-of-function mutations. Consequently, curators will need to use their expertise to determine whether interaction <br />
phenotypes resulting from gain-of-function mutations are informative about the normal, wild type role of a gene or gene product. <br />
<br />
'''Example 1: Double loss-of-function mutations resulting in enhancement of a mutant phenotype'''<br />
Localized cell wall degradation is essential for proper cell fusion in the fission yeast, ''Schizosaccharomyces pombe''. This <br />
process is accomplished by the localized action of degradative enzymes including several distinct glucanases that act on different<br />
polysaccharides. Deletion of multiple glucanases in ''S. pombe'' results in decreasing efficiency of cell fusion indicating that<br />
each enzyme contributes additively to this process.<br />
<br />
exg3 fungal-type cell wall disassembly involved in conjugation with cellular fusion (GO:1904541) PMID:25825517 IGI agn2<br />
agn2 fungal-type cell wall disassembly involved in conjugation with cellular fusion (GO:1904541) PMID:25825517 IGI exg3<br />
<br />
'''Example 2: Gain-of-function mutation''' <br />
The response to axonal injury requires the activities of MAP kinase and cAMP signaling pathways that are required, for example, for <br />
signaling growth cone formation. In C. elegans, the activity of the upstream-most kinase in one of the MAPK signaling pathways, <br />
DLK-1, is stimulated by Ca2+ influx mediated by the EGL-19 voltage-gated calcium channel. EGL-19’s regulatory role in the <br />
MAPK-mediated axon regeneration pathway was determined, in part, through doubly mutant animals containing an egl-19 gain-of-<br />
function mutation and a dlk-1 loss-of-function mutation that showed a reduced axon regenerative response when compared to <br />
egl-19(gf) alone. <br />
<br />
EGL-19 positive regulation of MAPK cascade involved in axon regeneration (GO:1904922) PMID:20203177 IGI DLK-1<br />
<br />
Note that in this example, reciprocal IGI annotations are not made, as the GO term selected for EGL-19 does not make sense for <br />
DLK-1.<br />
<br />
'''Example 3: Synergistic (synthetic) interactions'''<br />
Disruption of the MSB2 gene in S. cerevisiae has no appreciable effects on the cell's ability to activate the High-Osmolarity <br />
Glycerol (HOG) pathway upon osmotic stress, or on cellular growth on high-osmolarity media. To identify potential osmosensors in <br />
the SHO1 branch of the HOG pathway, the authors screened for a mutant that is osmosensitive only in an msb2Δ background and <br />
recovered mutations in the HKR1 gene. Like MSB2, mutations in HRK1 alone confer no osmosensitivity to the cells. <br />
<br />
MSB2 hyperosmotic response (GO:0006972) PMID:17627274 IGI HKR1<br />
HKR1 hyperosmotic response (GO:0006972) PMID:17627274 IGI MSB2<br />
<br />
'''Co-transfection experiments'''<br />
Co-transfection experiments include those experiments where two or more gene products are expressed in a heterologous system, such <br />
as a cell line, for the purposes of interrogating a functional interaction between them.<br />
<br />
In ''C. elegans'', the response to dauer pheromone, a mixture of small molecules, is mediated by G protein-coupled receptors <br />
(GPCRs). Genetic analysis has implicated two GPCRs, SRBC-64 and SRBC-66, in a signaling pathway that responds to specific<br />
components of dauer pheromone. To assess the biochemical role of SRBC-64 and SRBC-66, the gene products were expressed singly or<br />
in combination in HEK293 cells. Only when expressed in combination were the GPCRs able to enhance forskolin-stimulated cAMP<br />
production. <br />
<br />
SRBC-64 G-protein coupled receptor signaling pathway (GO:0007186) PMID:19797623 IGI SRBC-66<br />
SRBC-66 G-protein coupled receptor signaling pathway (GO:0007186) PMID:19797623 IGI SRBC-64<br />
<br />
'''Functional complementation'''<br />
Functional complementation refers to experiments in which a gene from one species complements a mutation in another. For <br />
these annotations, the With/From column should list the identifier for the endogenous gene that is complemented by the <br />
heterologously expressed gene being annotated. In annotations from cross-species functional complementation experiments, the gene <br />
referred to in the With/From column will thus be from a different species than the gene being annotated.<br />
<br />
'''Example'''<br />
''C. elegans'' contains two genes, lgg-1 and lgg-2, with sequence similarity to the ''Saccharomyces cerevisiae'' ubiquitin-like <br />
protein Atg8 that is required for autophagosome biogenesis. Transformation of lgg-1, but not lgg-2, into atg8 deletion mutants<br />
in nitrogen starvation medium results in increased survival compared to atg8 mutants alone, indicating that lgg-1 can functionally <br />
complement budding yeast atg8.<br />
<br />
lgg-1 macroautophagy (GO:0016236) PMID:20523114 IGI atg8<br />
<br />
'''Rescue experiments'''<br />
One way in which functional interactions between two or more genes is assessed is through phenotypic rescue experiments. In these <br />
experiments, the expression of one gene is used to complement, or rescue, the mutant phenotype resulting from mutations in a second<br />
gene. Rescue experiments may be used to help determine the order in which gene products act within a biological pathway or process.<br />
<br />
'''Example'''<br />
The planar cell polarity pathway is critical for a number of biological processes including epidermal wound repair. Activity of <br />
the GRHL3 transcription factor is essential for efficient wound repair in mice and human cell lines. Wound repair requires <br />
activation of the RhoA small GTPase to effect the cellular polarization, actin polymerization and epidermal migration critical to <br />
wound closure. The gene encoding the RhoGEF RhoGEF119, a RhoA GTPase activator, is a transcriptional target of GRHL3, and <br />
RHOGEF119 activity is also required for wound repair. Expression of human RhoGEF119 in human Grhl3-kd cell lines rescues the <br />
actin polymerization defects resulting from loss of Grhl13, indicating a role for RhoGEF119 in regulation of actin cytoskeletal<br />
organization during wound repair.<br />
<br />
ARHGEF19 positive regulation of actin cytoskeleton organization (GO:0032956) PMID:20643356 IGI GRHL3<br />
GRHL3 positive regulation of actin cytoskeleton organization (GO:0032956) PMID:20643356 IGI ARHGEF119<br />
<br />
'''When NOT to use IGI'''<br />
Some experiments assess a functional interaction between one or more gene products by examining the effects that mutations in one<br />
gene have on the properties of another. These types of experiments are annotated using the IMP (Inferred from Mutant Phenotype) <br />
evidence code and the target, or affected gene product, may be captured as an Annotation Extension. The key here is that the <br />
genetic perturbation is directed at only one of the gene products in the experiment. For example, treatment of cells with GSK3B <br />
antagonists results in nuclear accumulation of the GATA6 transcription factor. This experiment indicates that GSK3B negatively <br />
regulates GATA6 localization. <br />
<br />
GSK3B negative regulation of protein localization to nucleus (GO:1900181) PMID:23624080 transports_or_maintains_localization_of <br />
GATA6<br />
<br />
=Minutes=<br />
<br />
<br />
[[Category: Annotation Working Group]]</div>
Vanaukenk