search

geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
BSD 3-Clause "New" or "Revised" License
34 stars 10 forks source link

PTHR11309 PTN000139394/PTN000139395: smoothened receptors and frizzled receptors #1229

Closed gocentral closed 6 years ago

gocentral commented 9 years ago

Hi,

There are some issues with PTN000139394/PTN000139395 annotation of smoothened receptors and frizzled receptors

A. PTN000139394 smoothened receptors (AN1) which do not bind/act in the wnt signalling pathway have has terms from frizzled proteins/wnt signalling propagated to them.

e.g. D.mel P91682 smo GO:0017147 Wnt-protein binding GO:0030165 PDZ domain binding .......(can't find any literature on this for smo) GO:0042813 Wnt-activated receptor activity GO:0060070 canonical Wnt signaling pathway

B. PTN000139394 GO:0005737 cytoplasm - probably incorrect - any annotation may come from punctate staining associated with vesicles.

C. Over-specific process terms - too many terms, some of which quite specifc. PANTHER:PTN000139395 D.mel smo

GO:0001570 vasculogenesis GO:0002052 positive regulation of neuroblast proliferation GO:0003007 heart morphogenesis GO:0007368 determination of left/right symmetry ....... Not sure how conserved these pathways are, certainly not well characterised in flies GO:0010002 cardioblast differentiation GO:0021696 cerebellar cortex morphogenesis ....... D.mel doesn't have a cerebellar cortex GO:0021938 smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation ....... don't think that there are equivalent structures in flies GO:0031102 neuron projection regeneration GO:0043066 negative regulation of apoptotic process GO:0045880 positive regulation of smoothened signaling pathway ....... is in the pathway, not regulating GO:0048663 neuron fate commitment GO:0048846 axon extension involved in axon guidance GO:0060830 ciliary receptor clustering involved in smoothened signaling pathway

PANTHER:PTN000139394 (D.mel fz, fz2, fz3, fz4)

GO:0001944 vasculature development GO:0007420 brain development GO:0008406 gonad development

D. PANTHER:PTN000139394

GO:0042995 cell projection - a bit too vague to be propagated

Regards,

Helen

Reported by: hattrill

Original Ticket: geneontology/annotation-issues/1248

pgaudet commented 6 years ago

A. PTN000139394 smoothened receptors (AN1) which do not bind/act in the wnt signalling pathway have has terms from frizzled proteins/wnt signalling propagated to them. e.g. D.mel P91682 smo GO:0017147 Wnt-protein binding GO:0030165 PDZ domain binding .......(can't find any literature on this for smo) GO:0042813 Wnt-activated receptor activity GO:0060070 canonical Wnt signaling pathway

was removed

pgaudet commented 6 years ago

B. PTN000139394 GO:0005737 cytoplasm - probably incorrect - any annotation may come from punctate staining associated with vesicles.

was removed. Now this node is annotated to 'plasma membrane'

pgaudet commented 6 years ago

C. Over-specific process terms - too many terms, some of which quite specifc. PANTHER:PTN000139395 D.mel smo

No direct annotations. Inherited annotations are:

canonical Wnt signaling pathway non-canonical Wnt signaling pathway Wnt-protein binding central nervous system development smoothened signaling pathway dendrite morphogenesis of an epithelium cilium patched binding commissural neuron axon guidance positive regulation of smoothened signaling pathway

Should these be removed ?

pgaudet commented 6 years ago

C. continued: PANTHER:PTN000139394

(D.mel fz, fz2, fz3, fz4)

GO:0001944 vasculature development GO:0007420 brain development GO:0008406 gonad development

These annotations are gone.

pgaudet commented 6 years ago

D. PANTHER:PTN000139394 GO:0042995 cell projection - a bit too vague to be propagated

Gone as well.

pgaudet commented 6 years ago

@hattrill

Can you please check and close if all your queries have been addressed?

Thanks, Pascale

hattrill commented 6 years ago

Yep! All looks peachy. Thanks.