Annotation Conf. Call 2015-10-27: Difference between revisions
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- 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) | - 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 | {| class="wikitable" | ||
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| kctd10|| atrioventricular canal development|| GO:0036302|| IEP | |||
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- “negative regulation of transcription from RNA polymerase II promoter” (GO:0000122) based on the change in gene expression assessed by in situ hybridization (Fig2). | - “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: | examples: | ||
kctd10 negative regulation of transcription from RNA polymerase II promoter GO:0000122 IMP | {| class="wikitable" | ||
kctd10 negative regulation of transcription from RNA polymerase II promoter GO:0000122 | |- | ||
| kctd10|| negative regulation of transcription from RNA polymerase II promoter|| GO:0000122 || IMP || regulates_transcription_of (Has2)|regulates_transcription_of(anf)|regulates_transcripition_of(amhc)|regulates_transcripion_of(Bmp4)|regulates_transcription_of(Notch1b) || | |||
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| 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? | - Is there enough evidence for the following annotations? | ||
kctd10 eye development GO:0001654 IMP | |||
kctd10 head development GO:0060322 IMP | kctd10 eye development (GO:0001654) IMP | ||
kctd10 head development (GO:0060322) IMP | |||
It is possible that the eye/head phenotype is a secondary phenotype. | 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? | - The terms including “development”, “morphogenesis”, “formation” are confusing. What is the difference? Which one should we use in this context? | ||
Example: | Example: | ||
kctd10 endocardium development GO:0003157 IMP | {| class="wikitable" | ||
kctd10 endocardium morphogenesis GO:0003160 IMP | |- | ||
kctd10 endocardium formation GO:0060214 IMP | | kctd10 || endocardium development || GO:0003157 || IMP | ||
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| kctd10 || endocardium morphogenesis || GO:0003160 || IMP | |||
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| kctd10 || endocardium formation || GO:0060214 || IMP | |||
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- in Figure 3: hyaluronic acid staining was performed to visualize the cardiac jelly. | - in Figure 3: hyaluronic acid staining was performed to visualize the cardiac jelly. | ||
Annotation: | Annotation: | ||
kctd10 negative regulation of hyaluronan biosynthetic process GO:1900126 IMP | {| class="wikitable" | ||
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| kctd10|| negative regulation of hyaluronan biosynthetic process|| GO:1900126|| IMP | |||
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Is there enough evidence that kctd10 is involved in hyaluronan biosynthesis? | Is there enough evidence that kctd10 is involved in hyaluronan biosynthesis? | ||
Could it be possible that the increase in staining is a secondary effect? | Could it be possible that the increase in staining is a secondary effect? | ||
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- Should kct10 be annotated as “positive/negative regulation” of heart looping / atrioventricular canal development? | - Should kct10 be annotated as “positive/negative regulation” of heart looping / atrioventricular canal development? | ||
- Annotation: | - Annotation: | ||
has2 negative regulation of heart looping GO:1901208 IGI kctd10 | {| class="wikitable" | ||
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| has2 || negative regulation of heart looping || GO:1901208 || IGI || kctd10 | |||
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- Fig 5: regulation of transcription : which evidence code should be used? | - Fig 5: regulation of transcription : which evidence code should be used? |
Revision as of 19:59, 26 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 in gene
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? 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 Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA has_regulation_target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA tbx5a has_regulation _target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IGI tbx5a has_regulation _target(Tbx5a) kctd10 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 kctd10 transcription factor binding GO:0008134 IPI tbx5a kctd10 activating transcription factor binding GO:0033613 IPI ktcd10 RNA polymerase II activating transcription factor binding GO:0001102 IDA has_direct_input Tbx5 Kctd10 transcriptional repressor activity, RNA polymerase II transcription factor binding GO:0001191 IPI tbx5a