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Questions that arose during PAINT curation of the frizzled/SFRP family of Wnt receptors and their secreted counterparts
Questions for MOD curators
- Did anyone notice any papers where the Wnt interaction domain was mapped?
- All organisms with GO:0005515 "protein binding" annotations: Is there a more specific term you can use? Please particularly look for Wnt binding or PDZ domain binding.
- Important (not critical): Additional annotations to "PDZ domain binding" will help clarify how broadly the term should be propagated.
- Human: Check PMID 20802536, PMID 19388021, PMID 18953581, PMID 18256285
- Mammals: Check review PMID 19534027, PMID 17273804
- There are probably many others. A PubMed search for "frizzled PDZ" turned up ~42 hits.
- Critical : There are many annotations to "plasma membrane," but none to "integral to plasma membrane." Can anyone justify GO:0005887 "integral to plasma membrane"?
- Important (not critical) : There are annotations to "endosome" (or its children) for fly fz and fz2. Can anyone else make "endosome" annotations? It would help in determining whether to propagate it.
- Important (not critical): What are appropriate taxonomic ranges for the following terms. Are they mammal-specific?
- GO:0001553 "luteinization"
- GO:0042701 "progesterone secretion"
- GO:0046697 "decidualization"
- Fzd1 GO:0016481 "negative regulation of transcription" from PMID 16936075: Can you specify the child term GO:0010553 "negative regulation of gene-specific transcription from RNA polymerase II promoter"?
- Is GO:0021696 "cerebellar cortex morphogenesis" a valid annotation for flies? I.E., do flies have a cerebellar cortex?
Questions for ontology curators
- Should GO:0042813 "Wnt receptor activity" either is_a or has_part GO:0017147 "Wnt-protein binding"?
- Should GO:0005768 "endosome" be a child of GO:0030139 "endocytic vesicle"? Definitions:
- endocytic vesicle: A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance.
- endosome: A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
- Should there be a relationship between GO:0048786 "presynaptic active zone" and GO:0005938 "cell cortex"? Definitions:
- presynaptic active zone: A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, synaptic vesicles, and a specialized cortical cytoskeletal matrix.
- cell cortex: The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
- GO:0046329 "negative regulation of JNK cascade" and GO:0043508 "negative regulation of JUN kinase activity" are both children of GO:0046328 "regulation of JNK cascade." Shouldn't 43508 be a child of 46329, also?
- GO:0040025 "vulval development" is defined in terms of nematodes, despite the fact that they are not the only organism with a vulva. Should the name of the term be changed to "nematode vulval development" (with similar changes for its children)? Note that 40025 is a child of GO:0002119 "nematode larval development."
- GO:0046697 "decidualization" is defined as "The cellular and vascular changes occurring in the endometrium of the pregnant uterus just after the onset of blastocyst implantation..." However, the ontology does not reflect a relationship to any vascular process. Is there a link that can be made? Perhaps has_part GO:0001570 "vasculogenesis"?
- GO:0021508 "floor plate formation" is defined in terms of the neural tube, but the ontology shows it as a child of "neural plate formation" and not of "neural tube formation." Is this correct? (SF item # 3072034)
- Should GO:0060019 "radial glial cell differentiation" is_a GO:0010001 "glial cell differentiation"?