Annotation Conf. Call 2015-11-24
Meeting URL: https://bluejeans.com/993661940
Agenda
Annotation Consistency Exercise
Annotation consistency paper picked by TAIR: The MYB36 transcription factor orchestrates Casparian strip formation.
Choice of paper-motivation
Capturing downstream targets and their resulting effects, importance of reading term definitions
Annotations requested to be restricted to Figures 1-4 only, to keep discussion manageable.
Summary of the paper
MYB36 is a transcription factor that controls where the machinery for deposition/biosynthesis of lignin is expressed The location of the machinery determines where the Casparian strip can form.
Figure 1.
leaf ionome mutant vs. wt root hair phenotype mutant vs. wt endodermal localization of MYB36 expression
Figure 2.
Loss of Casparian strip and disruption of the apoplastic barrier in myb36 mutants.
Figure 3.
Identifying target genes of MYB36 - qPCR MYB36 binds specific target gene promoters - ChIP
Figure 4.
CASP1 localization Ectopic Casparian strip formation with induced ectopic expression of MYB36
Annotations:
Annotations received from five groups, TAIR included. (MGI, Pombase, WormBase, UCL)
Discussion points
Lots of new term requests. CASP1 and MYB36 annotated.
Molecular function
- transcription factor activity/sequence specific DNA binding
- review what to do with ChIP assays/chromatin binding
- review the relationship types for AE (has_input promoter, regulates_transcription_of, has_direct_input)
- IPI ok?
Cellular component
- nucleus?
Biological process
- secondary phenotypes? ionome and root hair differences - annotate?
- regulation of transcription
- regulation of protein localization?
- regulation of lignin/suberin biosynthesis
- (regulation of) Casparian strip formation
Minutes
In attendance
- Aleks, Alex, Chris, David H., Donghui, Edith, Elena, Kimberly, Leonore, Melanie, Midori, Pascale, Rachael, Robert, Sabrina, Stacia, Stan, Tanya, Val
Annotation Issues
Molecular Function
- Annotating ChIP experiments - still some discrepancy in how the results of these experiments are annotated
- There were a number of annotations to some flavor of DNA binding term, but we seem to agree that ChIP experiments don't allow for that level of resolution, i.e. what, exactly, does the target of the IP bind?
- Previously published guidelines for annotating transcription factors with GO terms