https://wiki.geneontology.org/index.php?title=PTHR12027&feed=atom&action=historyPTHR12027 - Revision history2024-03-29T15:18:59ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=PTHR12027&diff=74420&oldid=prevPascale at 14:34, 12 April 20192019-04-12T14:34:11Z<p></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>=PTHR12027 (Wnt family) tree annotation discussion=</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>=PTHR12027 (Wnt family) tree annotation discussion=</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 is a list of questions that arose while PAINTing the Wnt family. Please comment liberally, and please sign your comments. -Mike</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 is a list of questions that arose while PAINTing the Wnt family. Please comment liberally, and please sign your comments. -Mike</div></td></tr>
</table>Pascalehttps://wiki.geneontology.org/index.php?title=PTHR12027&diff=53232&oldid=prevGail at 22:33, 3 July 20142014-07-03T22:33:51Z<p></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>=PTHR12027 (Wnt family) tree annotation discussion=</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>=PTHR12027 (Wnt family) tree annotation discussion=</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 is a list of questions that arose while PAINTing the Wnt family. Please comment liberally, and please sign your comments. -Mike</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 is a list of questions that arose while PAINTing the Wnt family. Please comment liberally, and please sign your comments. -Mike</div></td></tr>
</table>Gailhttps://wiki.geneontology.org/index.php?title=PTHR12027&diff=30422&oldid=prevLn at 15:33, 26 August 20102010-08-26T15:33:58Z<p></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>*'''Question:''' Please verify the Wnt9a GO:0043028 "caspase regulator activity" annotation. Is this an actual molecular function of Wnt9a or just a downstream effect?</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>*'''Question:''' Please verify the Wnt9a GO:0043028 "caspase regulator activity" annotation. Is this an actual molecular function of Wnt9a or just a downstream effect?</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>**'''Curator answer:'''</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>**'''Curator answer:'''</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;">Yes, I made two annotations:</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>**<ins style="font-weight: bold; text-decoration: none;">The </ins>function <ins style="font-weight: bold; text-decoration: none;">annotation </ins>to GO:0043028 <ins style="font-weight: bold; text-decoration: none;">was deleted after a MGI group discussion</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;">***caspase regulator activity;</del></div></td><td colspan="2" class="diff-side-added"></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;">***negative regulation of caspase activity</del></div></td><td colspan="2" class="diff-side-added"></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;">**based on authors' statements, results' section "Reduction of caspase-3 activity by Wnt14", Fig. 3.</del></div></td><td colspan="2" class="diff-side-added"></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;">* '''(Question continued)''' Is this an actual molecular </del>function <del style="font-weight: bold; text-decoration: none;">of Wnt9a or just a downstream effect?</del></div></td><td colspan="2" class="diff-side-added"></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;">**Author use transfection experiments to assay effect "of Wnt14 on caspase-3 activity". In order to correspond to authors' statements, both annotations seem appropriate to me (Authors use term activity, not activation. I wanted to be close </del>to <del style="font-weight: bold; text-decoration: none;">authors' statements.) Whether it is a direct or indirect effect - I can not conclude from the presented data. Author discuss how exactly Wnt14 may be involved in caspase-3 regulation.</del></div></td><td colspan="2" class="diff-side-added"></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;">*'''Question follow-up''' (from Mike): Is this the MF </del>GO:0043028 <del style="font-weight: bold; text-decoration: none;">"caspase regulator activity" or the BP GO:0043281 "regulation of caspase activity"? If Wnt isn't actually touching caspase-3 -- and I think they're in separate compartments so they can't -- then it can't be the MF</del>. <del style="font-weight: bold; text-decoration: none;"> The downstream effect would have to be the BP, right?</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
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</table>Lnhttps://wiki.geneontology.org/index.php?title=PTHR12027&diff=30366&oldid=prevVarsha: /* All organisms */2010-08-25T10:23:22Z<p><span dir="auto"><span class="autocomment">All organisms</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>**from the wikipedia description of lipid rafts (http://en.wikipedia.org/wiki/Lipid_raft) I think that probably ISS of receptors to lipid rafts is OK. -- Ruth</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>**from the wikipedia description of lipid rafts (http://en.wikipedia.org/wiki/Lipid_raft) I think that probably ISS of receptors to lipid rafts is OK. -- Ruth</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>**If it is agreed that ligands can be annotated to the membrane, then I agree with the Wnt1/3 clade being annotated to membrane raft -- Varsha</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>**If it is agreed that ligands can be annotated to the membrane, then I agree with the Wnt1/3 clade being annotated to membrane raft -- Varsha</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>**1)The description of "lipid rafts" is not well-portrayed in the GO definition of "membrane raft." Wikipedia's is a more detailed/useful description; if accurate, maybe we should ask for a revision of the definition of membrane raft.</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>**1)The description of "lipid rafts" is not well-portrayed in the GO definition of "membrane raft." Wikipedia's is a more detailed/useful description; if accurate, maybe we should ask for a revision of the definition of membrane raft. <ins style="font-weight: bold; text-decoration: none;"> </ins>2) Regarding the query about "plasma membrane" as an annotation: Other than when I added the background info to the minutes from the meeting, there has been no further discussion of the issue, so I think it is unresolved. Personally, I think the definition of plasma membrane does include a ligand bound to a receptor, in part because there is a child term GO:0031236 "extrinsic to external side of plasma membrane, in periplasmic space" that seems at least as loosely bound to the membrane if not more so. It would be a true path violation if this term were not part of the plasma membrane. -- Mike</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>2) Regarding the query about "plasma membrane" as an annotation: Other than when I added the background info to the minutes from the meeting, there has been no further discussion of the issue, so I think it is unresolved. Personally, I think the definition of plasma membrane does include a ligand bound to a receptor, in part because there is a child term GO:0031236 "extrinsic to external side of plasma membrane, in periplasmic space" that seems at least as loosely bound to the membrane if not more so. It would be a true path violation if this term were not part of the plasma membrane. --Mike</div></td><td colspan="2" class="diff-side-added"></td></tr>
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</table>Varshahttps://wiki.geneontology.org/index.php?title=PTHR12027&diff=30365&oldid=prevVarsha: /* All organisms */2010-08-25T10:22:56Z<p><span dir="auto"><span class="autocomment">All organisms</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>*'''All''': There is 1 annotation to GO:0045121 "membrane raft" (Drosophila wingless, PMID 15166250). I've propagated it to the entire Wnt1/Wnt3 clade, but haven't found any other literature to support such an annotation for any Wnt. Comments would be appreciated.</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>*'''All''': There is 1 annotation to GO:0045121 "membrane raft" (Drosophila wingless, PMID 15166250). I've propagated it to the entire Wnt1/Wnt3 clade, but haven't found any other literature to support such an annotation for any Wnt. Comments would be appreciated.</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>**Curator answer: My understanding is that membrane rafts are quite specialised structures, so I would not annotate to the whole clade if there is no literature to support this in other species -- Varsha</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>**Curator answer: My understanding is that membrane rafts are quite specialised structures, so I would not annotate to the whole clade if there is no literature to support this in other species -- Varsha</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> </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>**from the wikipedia description of lipid rafts <ins style="font-weight: bold; text-decoration: none;">(http://en.wikipedia.org/wiki/Lipid_raft) </ins>I think that probably ISS of receptors to lipid rafts is OK. -- Ruth</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>**from the wikipedia description of lipid rafts I think that probably ISS of receptors to lipid rafts is OK. -- Ruth</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;">**If it is agreed that ligands can be annotated to the membrane, then I agree with the Wnt1/3 clade being annotated to membrane raft -- Varsha</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> </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;">**1)The description of "lipid rafts" is not well-portrayed in the GO definition of "membrane raft." Wikipedia's is a more detailed/useful description; if accurate, maybe we should ask for a revision of the definition of membrane raft.</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;">2) Regarding the query about "plasma membrane" as an annotation: Other than when I added the background info to the minutes from the meeting, there has been no further discussion of the issue, so I think it is unresolved. Personally, I think the definition of plasma membrane does include a ligand bound to a receptor, in part because there is a child term GO:0031236 "extrinsic to external side of plasma membrane, in periplasmic space" that seems at least as loosely bound to the membrane if not more so. It would be a true path violation if this term were not part of the plasma membrane. --Mike</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>Varshahttps://wiki.geneontology.org/index.php?title=PTHR12027&diff=30364&oldid=prevVarsha: /* All organisms */2010-08-25T10:11:21Z<p><span dir="auto"><span class="autocomment">All organisms</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 06:11, 25 August 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l41">Line 41:</td>
<td colspan="2" class="diff-lineno">Line 41:</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>*'''All''': There is 1 annotation to GO:0045121 "membrane raft" (Drosophila wingless, PMID 15166250). I've propagated it to the entire Wnt1/Wnt3 clade, but haven't found any other literature to support such an annotation for any Wnt. Comments would be appreciated.</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>*'''All''': There is 1 annotation to GO:0045121 "membrane raft" (Drosophila wingless, PMID 15166250). I've propagated it to the entire Wnt1/Wnt3 clade, but haven't found any other literature to support such an annotation for any Wnt. Comments would be appreciated.</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>**Curator answer: My understanding is that membrane rafts are quite specialised structures, so I would not annotate to the whole clade if there is no literature to support this in other species -- Varsha</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>**Curator answer: My understanding is that membrane rafts are quite specialised structures, so I would not annotate to the whole clade if there is no literature to support this in other species -- Varsha</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;">**from the wikipedia description of lipid rafts I think that probably ISS of receptors to lipid rafts is OK. -- Ruth</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>----</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>
</table>Varshahttps://wiki.geneontology.org/index.php?title=PTHR12027&diff=30307&oldid=prevLivstone: /* All organisms */2010-08-20T15:07:31Z<p><span dir="auto"><span class="autocomment">All organisms</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:07, 20 August 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l32">Line 32:</td>
<td colspan="2" class="diff-lineno">Line 32:</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>*'''All''': There are multiple annotations to "plasma membrane." Do you agree that this is valid for a ligand?</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>*'''All''': There are multiple annotations to "plasma membrane." Do you agree that this is valid for a ligand?</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>**Mike's comments:</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>**Mike's comments:</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>*** My main question is about the general permissibility of the term GO:0005886 "plasma membrane" for this purpose. It is defined as "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer '''and associated proteins'''." I think "associated" doesn't just mean "touching the bilayer" but also includes anything daisy-chained to it, in this case a ligand bound to a receptor which is integral to the membrane.</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>*** My main question is about the general permissibility of the term GO:0005886 "plasma membrane" for this purpose. It is defined as "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer '''and associated proteins'''." I think "associated" doesn't just mean "touching the bilayer" but also includes anything daisy-chained to it, in this case a ligand bound to a receptor which is integral to the membrane. <ins style="font-weight: bold; text-decoration: none;"> Based on </ins>this <ins style="font-weight: bold; text-decoration: none;">understanding</ins>, I propagated "plasma membrane" to all the Wnts. If the consensus is that this is not the proper meaning, then I'll remove that inference.</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;">*** My answer to </del>this <del style="font-weight: bold; text-decoration: none;">question was yes</del>, <del style="font-weight: bold; text-decoration: none;">and </del>I propagated "plasma membrane" to all the Wnts. If the consensus is that this is not the proper meaning, then I'll remove that inference.</div></td><td colspan="2" class="diff-side-added"></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>*** Here are the 3 examples (from 2 proteins) in the Wnt family:</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>*** Here are the 3 examples (from 2 proteins) in the Wnt family:</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>***# Rat Wnt7b, from PMID 18177422. I can't access the fulltext, so I can't assess it.</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>***# Rat Wnt7b, from PMID 18177422. I can't access the fulltext, so I can't assess it.</div></td></tr>
</table>Livstonehttps://wiki.geneontology.org/index.php?title=PTHR12027&diff=30306&oldid=prevLivstone: /* Mouse */2010-08-20T15:04:50Z<p><span dir="auto"><span class="autocomment">Mouse</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:04, 20 August 2010</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>* '''(Question continued)''' Is this an actual molecular function of Wnt9a or just a downstream effect?</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>* '''(Question continued)''' Is this an actual molecular function of Wnt9a or just a downstream effect?</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>**Author use transfection experiments to assay effect "of Wnt14 on caspase-3 activity". In order to correspond to authors' statements, both annotations seem appropriate to me (Authors use term activity, not activation. I wanted to be close to authors' statements.) Whether it is a direct or indirect effect - I can not conclude from the presented data. Author discuss how exactly Wnt14 may be involved in caspase-3 regulation.</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>**Author use transfection experiments to assay effect "of Wnt14 on caspase-3 activity". In order to correspond to authors' statements, both annotations seem appropriate to me (Authors use term activity, not activation. I wanted to be close to authors' statements.) Whether it is a direct or indirect effect - I can not conclude from the presented data. Author discuss how exactly Wnt14 may be involved in caspase-3 regulation.</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;">*'''Question follow-up''' (from Mike): Is this the MF GO:0043028 "caspase regulator activity" or the BP GO:0043281 "regulation of caspase activity"? If Wnt isn't actually touching caspase-3 -- and I think they're in separate compartments so they can't -- then it can't be the MF. The downstream effect would have to be the BP, right?</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>----</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"></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>Livstonehttps://wiki.geneontology.org/index.php?title=PTHR12027&diff=30304&oldid=prevLivstone: /* Cellular Component */2010-08-20T14:51:43Z<p><span dir="auto"><span class="autocomment">Cellular Component</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:51, 20 August 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l30">Line 30:</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>===All organisms===</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>===All organisms===</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>*'''All''': There are multiple annotations to "plasma membrane." Do you agree that this is valid for a ligand?</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>*'''All''': There are multiple annotations to "plasma membrane." Do you agree that this is valid for a ligand?</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;">**Mike's comments:</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;">*** My main question is about the general permissibility of the term GO:0005886 "plasma membrane" for this purpose. It is defined as "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer '''and associated proteins'''." I think "associated" doesn't just mean "touching the bilayer" but also includes anything daisy-chained to it, in this case a ligand bound to a receptor which is integral to the membrane.</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;">*** My answer to this question was yes, and I propagated "plasma membrane" to all the Wnts. If the consensus is that this is not the proper meaning, then I'll remove that inference.</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;">*** Here are the 3 examples (from 2 proteins) in the Wnt family:</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;">***# Rat Wnt7b, from PMID 18177422. I can't access the fulltext, so I can't assess it.</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;">***# Zebrafish wnt11, from PMID 17130287: "We show that in zebrafish embryonic cells, Wnt11 locally functions at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase cell contact persistence. This increase in cell contact persistence is mediated by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo at the plasma membrane, and it does not require the activity of further downstream effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence to coordinate cell movements during gastrulation."</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;">***# Zebrafish wnt11, from PMID 16198297: "Here, we show that Wnt11 functions during zebrafish gastrulation by regulating the cohesion of mesodermal and endodermal (mesendodermal) progenitor cells. Importantly, we demonstrate that Wnt11 activity in this process is mediated by the GTPase Rab5, a key regulator of early endocytosis, as blocking Rab5c activity in wild-type embryos phenocopies slb/wnt11 mutants, and enhancing Rab5c activity in slb/wnt11 mutant embryos rescues the mutant phenotype. In addition, we find that Wnt11 and Rab5c control the endocytosis of E-cadherin and are required in mesendodermal cells for E-cadherin-mediated cell cohesion. Together, our results suggest that Wnt11 controls tissue morphogenesis by modulating E-cadherin-mediated cell cohesion through Rab5c, a novel mechanism of Wnt signaling in gastrulation."</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;">So, it seems that they're saying that wnt11 persistently occupies the receptor and continues to carry out its signaling function.</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;"></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>*'''All''': There is 1 annotation to GO:0045121 "membrane raft" (Drosophila wingless, PMID 15166250). I've propagated it to the entire Wnt1/Wnt3 clade, but haven't found any other literature to support such an annotation for any Wnt. Comments would be appreciated.</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>*'''All''': There is 1 annotation to GO:0045121 "membrane raft" (Drosophila wingless, PMID 15166250). I've propagated it to the entire Wnt1/Wnt3 clade, but haven't found any other literature to support such an annotation for any Wnt. Comments would be appreciated.</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>**Curator answer: My understanding is that membrane rafts are quite specialised structures, so I would not annotate to the whole clade if there is no literature to support this in other species -- Varsha</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>**Curator answer: My understanding is that membrane rafts are quite specialised structures, so I would not annotate to the whole clade if there is no literature to support this in other species -- Varsha</div></td></tr>
</table>Livstonehttps://wiki.geneontology.org/index.php?title=PTHR12027&diff=30302&oldid=prevLivstone: /* Mouse and Rat */2010-08-20T14:15:18Z<p><span dir="auto"><span class="autocomment">Mouse and Rat</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:15, 20 August 2010</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>*'''Rat and Mouse''': Mouse Wnt7a has an annotation to GO:0050770 "regulation of axonogenesis." Rat Wnt7b has an annotation to GO:0032536 "regulation of cell projection size" from PMID 18177422; the abstract of this paper states, "Ectopic wnt7b overexpression was sufficient to rescue neurite outgrowth in NGF-treated p53-silenced PC12 cells." Is this sufficient to generalize "regulation of axonogenesis" to both Wnt 7a and -7b? Put another way, are PC12 "neurite outgrowths" sufficiently axon-like that this is probably the same 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>*'''Rat and Mouse''': Mouse Wnt7a has an annotation to GO:0050770 "regulation of axonogenesis." Rat Wnt7b has an annotation to GO:0032536 "regulation of cell projection size" from PMID 18177422; the abstract of this paper states, "Ectopic wnt7b overexpression was sufficient to rescue neurite outgrowth in NGF-treated p53-silenced PC12 cells." Is this sufficient to generalize "regulation of axonogenesis" to both Wnt 7a and -7b? Put another way, are PC12 "neurite outgrowths" sufficiently axon-like that this is probably the same process?</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>**'''Curator answer:'''MGI made the annotation according to paper PMID<del style="font-weight: bold; text-decoration: none;">: </del>9405095. It seems OK to me to generalize "regulation of axonogenesis" to both Wnt 7a and -7b.</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>**'''Curator answer:'''MGI made the annotation according to paper PMID 9405095. It seems OK to me to generalize "regulation of axonogenesis" to both Wnt 7a and -7b.</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>===Zebrafish===</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>===Zebrafish===</div></td></tr>
</table>Livstone