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

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Annotation consistency paper picked by TAIR:  [http://www.ncbi.nlm.nih.gov/pubmed/26124109 The MYB36 transcription factor orchestrates Casparian strip formation.]
Annotation consistency paper picked by TAIR:  [http://www.ncbi.nlm.nih.gov/pubmed/26124109 The MYB36 transcription factor orchestrates Casparian strip formation.]


'''Choice of paper-motivation''': capturing downstream targets and their resulting effects, importance of reading term definitions
===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.
Annotations requested to be restricted to Figures 1-4 only, to keep discussion manageable.


'''Summary of the paper'''
===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.
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.
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'''Annotations:'''
===Annotations:===


Annotations received from five groups, TAIR included.  (MGI, Pombase, WormBase, UCL)
Annotations received from five groups, TAIR included.  (MGI, Pombase, WormBase, UCL)




'''Discussion points'''
===Discussion points===


Lots of new term requests.
Lots of new term requests.


===Molecular function===
'''Molecular function'''


===Cellular component===
'''Cellular component'''


===Biological process===
'''Biological process'''





Revision as of 21:46, 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.

Molecular function

Cellular component

Biological process