Questions that arose during PAINT curation
Questions for MOD curators
- Should the Dicty aardvark protein be in this family?
- Mouse, rat, worm, and fly: Can you make the "protein binding" annotations more specific?
- All: Does Jup have DNA binding or transcription factor activity? Any annotations, positive or negative, would be very helpful.
- Mouse: Can you also make the Jup "protein binding" annotations more specific?
- Mouse: Does PMID 16973135 justify annotation to GO:0019903 "protein phosphatase binding" for Ctnnb1 in addition to Jup? The abstract states, "Glutathione-S-transferase (GST) pulldown assays were used to show that RPTPrho interacts with several adherens junctional proteins in brain, including E-cadherin, N-cadherin, VE-cadherin (cadherin-5), desmoglein, alpha, beta [Ctnnb1] and gamma [Jup] catenin, p120(ctn) and alpha-actinin." Would GO:0042153 "RPTP-like protein binding" be a better term?
- Human: The following GO terms are defined as containing beta-catenin. Should Ctnnb1 be annotated to them?
|Reference||GO term||Curator comment|
|PMID 9065401||GO:0070369 : beta-catenin-TCF7L2 complex||Have added this annotation|
|PMID 9065402||GO:0070369 : beta-catenin-TCF7L2 complex||This annotation already exists|
|PMID 16188939||GO:0034742 : APC-Axin-1-beta-catenin complex||Have added this annotation|
|PMID 16611247||GO:0034750 : Scrib-APC-beta-catenin complex||Have added this annotation to the mouse protein from this paper|
- Human: The following GO terms are defined as containing gamma-catenin. Should Jup be annotated to them?
|Reference||GO term||Curator comment|
|PMID 14661054||GO:0071664 : catenin-TCF7L2 complex||This annotation already exists|
|PMID 14661054||GO:0071665 : gamma-catenin-TCF7L2 complex||Have modified the annotation above to this more specific child term|
- Mouse: Please verify any beta catenin annotations from MGI:3610682/PMID 16339037. I can't find the gene mentioned anywhere in the paper.
J number typo, fixed
- Mouse: Please check the GO:0045177 "apical part of cell" annotation from MGI:3037622/PMID 15037549, which states, "beta-catenin, f-actin, and myosin II-B localize predominantly to the apical–junctional complex in normal neuroepithelium (Fig. 6E–G)." Is there additional supporting evidence for the 45177 annotation? Note that GO:0043296 "apical junction complex" is not part of 45177.
MGI annotated to both GO:0045177 and GO:0043296. Yes, there is additional supporting evidence for GO:0045177 annotation from the paper.
- Fly: Please check figure 4 of PMID 9657150 to verify the GO:0016324 "apical plasma membrane" annotation. Does the figure really show that armadillo is found in the apical region of the cell, or at apical junctions, which are not part of the apical region. The caption states, "In the larval eye disc, Arm is present at the apical junctions of all epithelial cells but concentrated at points of photoreceptor contact." Does the later statement "D-APC and Arm are both found apically within photoreceptor cells" actually refer to 16324 or is it shorthand for the junction?
- Mouse Jup: Can you annotate to GO:0007016 "cytoskeletal anchoring at plasma membrane" based on PMID 18496566?
- Mouse Ctnnb1: Instead of GO:0048593 "camera-type eye morphogenesis" would you prefer GO:0002089 "lens morphogenesis in camera-type eye" based on PMID 16102745, "The duality of beta-catenin function: a requirement in lens morphogenesis and signaling suppression of lens fate in periocular ectoderm"?
- Mouse Ctnnb1: Is the GO:0045453 "bone resorption" annotation from PMID 15866165 correct, or is it the phenotype of a beta catenin knockout? See the section entitled "Low Bone Mass and High Bone Resorption in Mice Lacking ?-Catenin in Osteoblasts."
This paper also shows that the Ctnnb1 directly affects the control of differentiation of osteoclasts, MGI is going to keep this annotation (Osteoclasts are the cells that absorb bone).
- Mouse Ctnnb1: Would you like to specify "lung" for the two GO:0002053 "positive regulation of mesenchymal cell proliferation" annotations (PMID 18231602 and PMID 18533146)?
- Mouse Ctnnb1: Please verify the GO:0035117 "embryonic arm morphogenesis" annotation from PMID 15371327. Is it conventional to refer to the mouse forelimb as an arm?
This is OK even though the mouse is a quadriped, from an embryonic standpoint the forelegs are the same as 'arms' and the hindlegs are the same as 'legs'.
- Mouse Ctnnb1: Is GO:0050909 "sensory perception of taste" actually shown in PMID 17128274? The paper seems to be all about taste bud development. Note that the definition includes "This is a neurological process."
Questions for ontology curators
- GO:0042153 "RPTP-like protein binding" is not a child of GO:0019903 "protein phosphatase binding," presumably because the definition of 42153 does not require that the protein in question be a phosphatase but rather have "similar structure/function to receptor protein tyrosine phosphatases." So, how do you annotate binding to a protein that is like RPTP and is a known phosphatase?
- Please clarify the definition of GO:0030057 "desmosome." Does the desmosome include the associated intermediate filaments?
- Should GO:0033077 "T cell differentiation in the thymus" be part_of GO:0048538 "thymus development"???