Annotation Conf. Call 2015-11-24

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