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

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(Annotation Consistency Exercise)
(Annotation Consistency Exercise)
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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.  
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Figure 4. (a,f) The endocardium of the mutant was extremely shrunken and the space between the myocardium and endocardium was much wider than that of the wild-type.
  
 
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Revision as of 06:39, 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.

Figure 4. (a,f) The endocardium of the mutant was extremely shrunken and the space between the myocardium and endocardium was much wider than that of the wild-type.

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