Annotation Conf. Call 2015-11-24: Difference between revisions

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Lots of new term requests.
Lots of new term requests.
CASP1 and MYB36 annotated.


'''Molecular function'''
'''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'''
'''Cellular component'''
nucleus?


'''Biological process'''
'''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





Revision as of 21:55, 23 November 2015

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