https://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&feed=atom&action=historyIndirectly positively regulates - Revision history2024-03-28T08:57:58ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=85099&oldid=prevPascale: /* Overview and Scope of Use */2023-03-16T17:25:43Z<p><span dir="auto"><span class="autocomment">Overview and Scope of Use</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>== Overview and Scope of Use==</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>== Overview and Scope of Use==</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation links two activities when the first activity has a positive regulatory effect on the second activity via a larger process (module) that is reused in many contexts, <del style="font-weight: bold; text-decoration: none;">and the curator does </del>not <del style="font-weight: bold; text-decoration: none;">want </del>to <del style="font-weight: bold; text-decoration: none;">reproduce that </del>module in <del style="font-weight: bold; text-decoration: none;">this </del>GO-CAM. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the upstream activity to a a regulation biological process term (e.g. regulation of transcription has_input target gene) to capture which process is left out of the model.</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>*This relation links two activities when the first activity has a positive regulatory effect on the second activity via a larger process (module) that is reused in many contexts<ins style="font-weight: bold; text-decoration: none;">. In this case</ins>, <ins style="font-weight: bold; text-decoration: none;">curators are </ins>not <ins style="font-weight: bold; text-decoration: none;">required </ins>to <ins style="font-weight: bold; text-decoration: none;">model the larger process (</ins>module<ins style="font-weight: bold; text-decoration: none;">) </ins>in <ins style="font-weight: bold; text-decoration: none;">every </ins>GO-CAM <ins style="font-weight: bold; text-decoration: none;">that refers to it</ins>. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the upstream activity to a a regulation biological process term (e.g. regulation of transcription has_input target gene) to capture which process is left out of the model.</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>*The 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</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 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</div></td></tr>
</table>Pascalehttps://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=85089&oldid=prevPascale: /* Overview and Scope of Use */2023-03-16T14:22:17Z<p><span dir="auto"><span class="autocomment">Overview and Scope of Use</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:22, 16 March 2023</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>== Overview and Scope of Use==</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>== Overview and Scope of Use==</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation links two activities <del style="font-weight: bold; text-decoration: none;">where </del>the first activity has a positive regulatory effect on the second activity via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the upstream activity to a a regulation biological process term (e.g. regulation of transcription has_input target gene) to capture which process is left out of the model.</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>*This relation links two activities <ins style="font-weight: bold; text-decoration: none;">when </ins>the first activity has a positive regulatory effect on the second activity via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the upstream activity to a a regulation biological process term (e.g. regulation of transcription has_input target gene) to capture which process is left out of the model.</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>*The 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</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 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</div></td></tr>
</table>Pascalehttps://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=85079&oldid=prevPascale: /* Overview and Scope of Use */2023-03-16T13:03:43Z<p><span dir="auto"><span class="autocomment">Overview and Scope of Use</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:03, 16 March 2023</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>== Overview and Scope of Use==</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>== Overview and Scope of Use==</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation links <del style="font-weight: bold; text-decoration: none;">tow Molecular Functions in which </del>the first <del style="font-weight: bold; text-decoration: none;">MF </del>has a positive regulatory effect on the second <del style="font-weight: bold; text-decoration: none;">MF </del>via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the upstream activity to a a regulation biological process term (e.g. regulation of transcription has_input target gene) to capture which process is left out of the model.</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>*This relation links <ins style="font-weight: bold; text-decoration: none;">two activities where </ins>the first <ins style="font-weight: bold; text-decoration: none;">activity </ins>has a positive regulatory effect on the second <ins style="font-weight: bold; text-decoration: none;">activity </ins>via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the upstream activity to a a regulation biological process term (e.g. regulation of transcription has_input target gene) to capture which process is left out of the model.</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>*The 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</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 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</div></td></tr>
</table>Pascalehttps://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=85078&oldid=prevPascale: /* Overview and Scope of Use */2023-03-16T13:01:14Z<p><span dir="auto"><span class="autocomment">Overview and Scope of Use</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:01, 16 March 2023</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>== Overview and Scope of Use==</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>== Overview and Scope of Use==</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation <del style="font-weight: bold; text-decoration: none;">is intended to represent </del>a positive regulatory effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the upstream activity to a a regulation biological process term (e.g. regulation of transcription has_input target gene) to capture which process is left out of the model.</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>*This relation <ins style="font-weight: bold; text-decoration: none;">links tow Molecular Functions in which the first MF has </ins>a positive regulatory effect <ins style="font-weight: bold; text-decoration: none;">on the second MF </ins>via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the upstream activity to a a regulation biological process term (e.g. regulation of transcription has_input target gene) to capture which process is left out of the model.</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>*The 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</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 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</div></td></tr>
</table>Pascalehttps://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=84653&oldid=prevVanaukenk: /* Review Status */2023-02-15T20:35:39Z<p><span dir="auto"><span class="autocomment">Review Status</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:35, 15 February 2023</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>== Review Status ==</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 Status ==</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>Last reviewed: February <del style="font-weight: bold; text-decoration: none;">7</del>, 2023</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>Last reviewed: February <ins style="font-weight: bold; text-decoration: none;">15</ins>, 2023</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>Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Sylvain Poux, Paul Thomas, Kimberly Van Auken </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>Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Sylvain Poux, Paul Thomas, Kimberly Van Auken </div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=84652&oldid=prevVanaukenk: /* Example */2023-02-15T20:35:30Z<p><span dir="auto"><span class="autocomment">Example</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" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A63d320cd00000458 <del style="font-weight: bold; text-decoration: none;">Example </del>GO-CAM]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A63d320cd00000458 GO-CAM <ins style="font-weight: bold; text-decoration: none;">model</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>== Relations Ontology ==</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>== Relations Ontology ==</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=84651&oldid=prevVanaukenk: /* Annotation Usage Guidelines */2023-02-15T20:34:46Z<p><span dir="auto"><span class="autocomment">Annotation Usage Guidelines</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>== Annotation Usage Guidelines ==</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>== Annotation Usage Guidelines ==</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>*'''What to capture'''</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>*'''What to capture'''</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>** This relation is typically used for <del style="font-weight: bold; text-decoration: none;">MFs </del>that are part of activity-regulating BPs, e.g. regulation of gene expression and its children, that increase expression and thus, activity, of the downstream target.</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>** This relation is typically used for <ins style="font-weight: bold; text-decoration: none;">activities </ins>that are part of activity-regulating BPs, e.g. regulation of gene expression and its children, that increase expression and thus, activity, of the downstream target.</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>*'''What to capture'''</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>*'''What to capture'''</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>** Indirectness indicates that there are intervening activities, e.g. general transcription factor activities <del style="font-weight: bold; text-decoration: none;">or endoribonucleases</del>, between the two activities connected with this relation. Since the intervening activities may be part of a larger coordinated process of gene expression, it is not necessary for curators to model the entire coordinated process in their GO-CAM.</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>** Indirectness indicates that there are intervening activities, e.g. general transcription factor activities, between the two activities connected with this relation. Since the intervening activities may be part of a larger coordinated process of gene expression, it is not necessary for curators to model the entire coordinated process in their GO-CAM.</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>== Example == </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>== Example == </div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=84650&oldid=prevVanaukenk: /* Overview and Scope of Use */2023-02-15T20:33:51Z<p><span dir="auto"><span class="autocomment">Overview and Scope of Use</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>== Overview and Scope of Use==</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>== Overview and Scope of Use==</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation is used in GO-CAMs but not in standard annotation extensions.</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>*This relation is intended to represent a positive regulatory effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the activity to <del style="font-weight: bold; text-decoration: none;">GO:xxxxx </del>(regulation of <del style="font-weight: bold; text-decoration: none;">gene expression </del>has_input target gene) to capture which process is left out of the model.</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>*This relation is intended to represent a positive regulatory effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the <ins style="font-weight: bold; text-decoration: none;">upstream </ins>activity to <ins style="font-weight: bold; text-decoration: none;">a a regulation biological process term </ins>(<ins style="font-weight: bold; text-decoration: none;">e.g. </ins>regulation of <ins style="font-weight: bold; text-decoration: none;">transcription </ins>has_input target gene) to capture which process is left out of the model.</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>*The 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</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 'indirectly positively regulates' relation is used to relate two GO molecular functions when:</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=84171&oldid=prevPascale: /* Example */2023-02-07T17:08:49Z<p><span dir="auto"><span class="autocomment">Example</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>C. elegans DAF-16 is required for transcription of the cyclin-dependent kinase inhibitor cki-1 in stem cells in response to starvation. In starved daf-16(mgDf50) L1 larvae, physiologically regulated cki-1::GFP expression is absent or diminished in V lineage seam cells, indicating that DAF-16 is required for physiologically regulated expression of cki-1::GFP. In the corresponding GO-CAM model of negative regulation of nematode larval development in response to starvation, DAF-16 thus indirectly positively regulates the cyclin-dependent serine/threonine kinase inhibitor activity of CKI-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>C. elegans DAF-16 is required for transcription of the cyclin-dependent kinase inhibitor cki-1 in stem cells in response to starvation. In starved daf-16(mgDf50) L1 larvae, physiologically regulated cki-1::GFP expression is absent or diminished in V lineage seam cells, indicating that DAF-16 is required for physiologically regulated expression of cki-1::GFP. In the corresponding GO-CAM model of negative regulation of nematode larval development in response to starvation, DAF-16 thus indirectly positively regulates the cyclin-dependent serine/threonine kinase inhibitor activity of CKI-1.</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> </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> </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>[[File:Indirect_pos<del style="font-weight: bold; text-decoration: none;">.png</del>.png|500px|Indirectly positively regulates GO-CAM example]]</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>[[File:Indirect_pos.png|500px|Indirectly positively regulates GO-CAM example]]</div></td></tr>
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</table>Pascalehttps://wiki.geneontology.org/index.php?title=Indirectly_positively_regulates&diff=84170&oldid=prevPascale: /* Example */2023-02-07T17:08:37Z<p><span dir="auto"><span class="autocomment">Example</span></span></p>
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</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l18">Line 18:</td>
<td colspan="2" class="diff-lineno">Line 18:</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>C. elegans DAF-16 is required for transcription of the cyclin-dependent kinase inhibitor cki-1 in stem cells in response to starvation. In starved daf-16(mgDf50) L1 larvae, physiologically regulated cki-1::GFP expression is absent or diminished in V lineage seam cells, indicating that DAF-16 is required for physiologically regulated expression of cki-1::GFP. In the corresponding GO-CAM model of negative regulation of nematode larval development in response to starvation, DAF-16 thus indirectly positively regulates the cyclin-dependent serine/threonine kinase inhibitor activity of CKI-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>C. elegans DAF-16 is required for transcription of the cyclin-dependent kinase inhibitor cki-1 in stem cells in response to starvation. In starved daf-16(mgDf50) L1 larvae, physiologically regulated cki-1::GFP expression is absent or diminished in V lineage seam cells, indicating that DAF-16 is required for physiologically regulated expression of cki-1::GFP. In the corresponding GO-CAM model of negative regulation of nematode larval development in response to starvation, DAF-16 thus indirectly positively regulates the cyclin-dependent serine/threonine kinase inhibitor activity of CKI-1.</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> </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> </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>[[File:<del style="font-weight: bold; text-decoration: none;">Constitutively upstream</del>.png|500px|<del style="font-weight: bold; text-decoration: none;">Indirect_pos.png</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>[[File:<ins style="font-weight: bold; text-decoration: none;">Indirect_pos.png</ins>.png|500px|<ins style="font-weight: bold; text-decoration: none;">Indirectly positively regulates GO-CAM example</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>
</table>Pascale