Difference between revisions of "Annotation Conf. Call 2015-10-27"

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- The terms including “development”, “morphogenesis”, “formation” are confusing. What is the difference? Which one should we use in this context?  
 
- The terms including “development”, “morphogenesis”, “formation” are confusing. What is the difference? Which one should we use in this context?  
 +
 
- Statements from paper:
 
- Statements from paper:
 +
 
Figure 1. (i-k) Both the myocardium (green) and the endocardium (red) are substantially smaller in the mutant and the morphant, and no cavity is visible inside the heart lumen.  
 
Figure 1. (i-k) Both the myocardium (green) and the endocardium (red) are substantially smaller in the mutant and the morphant, and no cavity is visible inside the heart lumen.  
 
Example:  
 
Example:  

Revision as of 07:34, 27 October 2015

Meeting URL: https://bluejeans.com/993661940

Agenda

Annotation Consistency Exercise

Annotation consistency paper picked by ZFIN- PMID:24430697

Choice of paper-motivation: discussing the use of IGI as evidence code. When should we use IGI?

- mutation in gene A is rescued by a mutation in gene B
- mutation in gene A is rescued by over-expression of gene B

In this paper, how do we capture

- the repression of transcriptional activation activity of tbx5a by kctd10?
- the information about has2

Summary of the paper (PMID:24430697)

- mutants in kctd10 show heart defects (heart looping, atrioventricular canal development)

Note: phenotypes determined by

- analysis of heart morphology
- gene expression analysis of genes known to be expressed in specific part of the heart).

[Fig 1, 2, 3]

- downregulation of tbx5a or has 2 (using MO) rescue kctd10 mutant heart phenotypes. [Fig 4]

- in vitro experiments [Fig5]:

- luciferase reporter assay
kctd10 inhibits tbx5 transcriptional activity
- Co-IP ; Pull down assay:
tbx5a and kctd10 physically interact with each other.

Annotations: 9 sets of annotations received.

Analysis and points of discussion: (in no particular order)

- Most of us annotated kct10 to heart looping/atrioventricular canal development with IMP

- Use of IEP: One annotation used IEP (Inferred from Expression Pattern) as evidence code because the annotation based on altered expression of AVC marker genes (Fig 2)

kctd10 atrioventricular canal development GO:0036302 IEP

- “negative regulation of transcription from RNA polymerase II promoter” (GO:0000122) based on the change in gene expression assessed by in situ hybridization (Fig2). examples:

kctd10 negative regulation of transcription from RNA polymerase II promoter GO:0000122 IMP regulates_transcription_of(anf)|regulates_transcripition_of(amhc)|regulates_transcripion_of(Bmp4)|regulates_transcription_of(Notch1b)
kctd10 negative regulation of transcription from RNA polymerase II promoter GO:0000122 IMP regulates_transcription_of: tbx2b, occurs_in myocardium, happens_during cardiac chamber morphogenesis


- Is there enough evidence for the following annotations?

kctd10 eye development GO:0001654 IMP
kctd10 head development GO:0060322 IMP


It is possible that the eye/head phenotype is a secondary phenotype.

- The terms including “development”, “morphogenesis”, “formation” are confusing. What is the difference? Which one should we use in this context?

- Statements from paper:

Figure 1. (i-k) Both the myocardium (green) and the endocardium (red) are substantially smaller in the mutant and the morphant, and no cavity is visible inside the heart lumen. Example:

kctd10 endocardium development GO:0003157 IMP
kctd10 endocardium morphogenesis GO:0003160 IMP
kctd10 endocardium formation GO:0060214 IMP

- in Figure 3: hyaluronic acid staining was performed to visualize the cardiac jelly. Annotation:

kctd10 negative regulation of hyaluronan biosynthetic process GO:1900126 IMP

Is there enough evidence that kctd10 is involved in hyaluronan biosynthesis? Could it be possible that the increase in staining is a secondary effect?

- Fig4: injection of tbx5MO and has2MO rescue kctd10 mutant phenotype: Most of us annotated using IGI between tbx5 and kctd10, and between has2 and kctd10 heart looping/atrioventricular canal development

- Should kct10 be annotated as “positive/negative regulation” of heart looping / atrioventricular canal development?

- Annotation:

has2 negative regulation of heart looping GO:1901208 IGI kctd10

- Fig 5: regulation of transcription : which evidence code should be used?

kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA
kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA has_regulation_target(Tbx5a)
kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA tbx5a has_regulation _target(Tbx5a)
kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IGI tbx5a has_regulation _target(Tbx5a)
kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IMP has_regulation_target: tbx5b

- protein binding: which evidence code should be used? examples:

kct10 protein binding GO:0005515 IPI tbx5a
kct10 transcription factor binding GO:0008134 IPI tbx5a
kct10 activating transcription factor binding GO:0033613 IPI
kct10 RNA polymerase II activating transcription factor bindin GO:0001102 IDA has_direct_input Tbx5
kct10 transcriptional repressor activity, RNA polymerase II transcription factor binding GO:0001191 IPI tbx5a

Minutes