Annotation Conf. Call 2017-02-28: Difference between revisions

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*[http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00000338 myo2_rlc1_PMID19570908]
*[http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00000338 myo2_rlc1_PMID19570908]
*[https://www.ncbi.nlm.nih.gov/pubmed/19570908 Regulation of fission yeast myosin-II function and contractile ring dynamics by regulatory light-chain and heavy-chain phosphorylation.]
*[https://www.ncbi.nlm.nih.gov/pubmed/19570908 Regulation of fission yeast myosin-II function and contractile ring dynamics by regulatory light-chain and heavy-chain phosphorylation.]
*In vitro and in vivo assays using nonphosphorylatable or phosphomimetic Rlc1 mutations show that Rlc1 somehow positively regulates the actin filament-based motor activity of Myo2 as part of actomyosin contractile ring contraction, in turn part of mitotic cytokinesis.
**We were very tempted to say that Rlc1's unknown MF regulator activity directly positively regulates Myo2's microfilament motor activity because:
*** Rlc1 has previously been shown to bind Myo2;
*** The in vitro assays (Fig.1, Table 3) show an effect on Myo2 motor activity with only F-actin, Myo2, Cdc4. and Rlc1 (heavy chain, essential light chain, and regulatory light chains respectively) present.
**The reason we didn't, and instead included the actin filament-based movement "link", is that the is_a hierarchy has motor activity as a subtype of NTPase activity:
<nowiki>
    GO:0017111 ! nucleoside-triphosphatase activity
    -- is_a GO:0003774 ! motor activity
    ---- is_a GO:0000146 ! microfilament motor activity
</nowiki>
:*From this, reasoning would infer this regulation hierarchy (whether regulation terms are instantiated or not):
<nowiki>
    regulation of nucleoside-triphosphatase activity
    -- is_a regulation of motor activity
    ---- is_a regulation of microfilament motor activity
</nowiki>
:*... and erroneously conclude that Rlc1 does regulate Myo2's ATPase activity. The Rlc1 mutant phenotypes here say it doesn't (Fig. 76, Table 3).
*Questions:
**Should the MF ontology change to motor activity has_part nucleoside-triphosphatase activity?
**Does LEGO have any way to capture when a molecular mechanism isn't known, but one possibility has been ruled out?
=== April Discussion ===
=== April Discussion ===
*April 25th
*April 25th

Revision as of 11:20, 27 February 2017

Bluejeans URL

https://bluejeans.com/993661940

Agenda

GO Meeting Reminder

Noctua Modeling Discussion

Sabrina Toro, Zfin

Midori Harris, PomBase

  • myo2_rlc1_PMID19570908
  • Regulation of fission yeast myosin-II function and contractile ring dynamics by regulatory light-chain and heavy-chain phosphorylation.
  • In vitro and in vivo assays using nonphosphorylatable or phosphomimetic Rlc1 mutations show that Rlc1 somehow positively regulates the actin filament-based motor activity of Myo2 as part of actomyosin contractile ring contraction, in turn part of mitotic cytokinesis.
    • We were very tempted to say that Rlc1's unknown MF regulator activity directly positively regulates Myo2's microfilament motor activity because:
      • Rlc1 has previously been shown to bind Myo2;
      • The in vitro assays (Fig.1, Table 3) show an effect on Myo2 motor activity with only F-actin, Myo2, Cdc4. and Rlc1 (heavy chain, essential light chain, and regulatory light chains respectively) present.
    • The reason we didn't, and instead included the actin filament-based movement "link", is that the is_a hierarchy has motor activity as a subtype of NTPase activity:
     GO:0017111 ! nucleoside-triphosphatase activity
     -- is_a GO:0003774 ! motor activity
     ---- is_a GO:0000146 ! microfilament motor activity
  • From this, reasoning would infer this regulation hierarchy (whether regulation terms are instantiated or not):
     regulation of nucleoside-triphosphatase activity
     -- is_a regulation of motor activity
     ---- is_a regulation of microfilament motor activity
  • ... and erroneously conclude that Rlc1 does regulate Myo2's ATPase activity. The Rlc1 mutant phenotypes here say it doesn't (Fig. 76, Table 3).
  • Questions:
    • Should the MF ontology change to motor activity has_part nucleoside-triphosphatase activity?
    • Does LEGO have any way to capture when a molecular mechanism isn't known, but one possibility has been ruled out?

April Discussion

Minutes

  • On call:
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