Annotation Conf. Call 2015-10-27
Meeting URL: https://bluejeans.com/993661940
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:
- 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?
|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||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|