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: Barbara, David H., Edith, Giulia, Harold, Helen, Karen, Kimberly, Li, Midori, Pascale, Paul, Ruth, Sabrina, Stacia, Stan, Tanya, Terry
Noctua Modeling
- Sabrina (Zfin) - role of TFs in neutrophil maturation
- Two TFs, C-myb and Cebp1
- Represent TFs with MF term for transcription factor activity, sequence-specific DNA binding
- Indicate gene promoter bound with has_input (lyz)
- occurs_in:
- chromatin - based on ChIp assay
- part_of:
- transcription - based on direct assays and mutant phenotypes
- transcription factor complex
- based on co-IP of C-myb and Cebp1
- There is no information about the precise role of lyz in neutrophil maturation
- Transcription part_of cell maturation
- Based on mutant phenotype
- Neutrophil maturation didn't exist in GO
- Created term by linking cell maturation 'results in maturation of' neutrophil
- Evidence was direct assay based on what the authors show about this process
- Questions:
- Harold - transcription factor complex - why is there a separate individual for the complex as well as both each TFs separately?
- Sabrina - this is what the data suggested
- Karen - can use the more specific RNA polII transcription factor activity?
- Sabrina - Yes, could do this.
- Kimberly - Might be a nice check to have to prompt curators to use the more specific MF term when the more specific BP term is also used.
- David - What would the reasoner give if we run it?
- Paul T. - The coming design templates should include transcription and will give curators a standard way to annotate these things. Curators will then just need to fill in the specific entities and evidence.
- Tried running the reasoner