Annotation Conf. Call 2017-02-28: Difference between revisions
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= Minutes = | = Minutes = | ||
*On call: | *On call: David H., Kimberly, Sabrina | ||
[[Category: Annotation Working Group]] | [[Category: Annotation Working Group]] |
Revision as of 11:58, 28 February 2017
Bluejeans URL
https://bluejeans.com/993661940
Agenda
GO Meeting Reminder
- Corvallis, Oregon - June 1-3rd, Noctua Workshop - June 4th, Reactome Workshop - June 5th
- Meeting Registration Site
- Meeting Agenda
Noctua Modeling Discussion
Sabrina Toro, Zfin
- ZDB-PUB-160610-16 myb, cebp1 and neutrophil maturation
- c-Myb acts in parallel and cooperatively with Cebp1 to regulate neutrophil maturation in zebrafish.
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:
- We were very tempted to say that Rlc1's unknown MF regulator activity directly positively regulates Myo2's microfilament motor activity because:
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
- April 25th
- Sign up: LEGO Discussion Rota
Minutes
- On call: David H., Kimberly, Sabrina