regulation of cardiomyocyte membrane depolarizat

[gocentral]

Hi David

I have requested some terms via term genie, but I don't think these really fit in with normal GO.

The regulation terms have numbers around GO:1900827

I wanted to annotate the rat Ank3 gene based on the data in PMID:18180363 which shows that this gene is involved in transporting SLC5A to the cell surface, and that sodium transport is reduced when Ank3 is knocked down.

At present we have GO:0086012 membrane depolarization involved in regulation of cardiac muscle cell action potential is_a >GO:0060373 regulation of ventricular cardiomyocyte membrane depolarization

However, I wasn't sure that the cardiomyocytes used in Figure 5 (which demonstrates effect of Ank3 depletion on sodium current) are ventricular cardiomyocyte (although ventricular cardiomyocytes do appear to be used in Figure 8, which confirms Ank3 and ANK3 are necessary for SLC5A localization to plasma membrane).

Therefore I was looking for the term positive regulation of cardiomyocyte membrane depolarization (plus reg and neg terms?) as a pos reg child of GO:0086012 membrane depolarization involved in regulation of cardiac muscle cell action potential

The new term regulation of cardiomyocyte membrane depolarization would be a parent of GO:0060373 regulation of ventricular cardiomyocyte membrane depolarization and the atrial term too.

Anyway, that is assuming that you agree that proteins involved in placing the channels in the membrane should be annotated to regulation of depolarisation?

So I am not sure if you want to rename the term genie terms I created or if you want to delete those terms and start again

Sorry not to have just submitted this in the first place, or added this info in the notes field

Ruth

Reported by: RLovering

Original Ticket: geneontology/ontology-requests/9520

[gocentral]

Hi Ruth and David,

I'm assigning this to David then. David, feel free to let me know otherwise.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• assigned_to: nobody --> ukemi

Original comment by: paolaroncaglia

[gocentral]

Hi Ruth,

Would it make sense to add the generic non-ventricular terms and then make the TG terms children of them? I think all of the generic terms could be made by TG, but would have to take a closer look. I think you want the ventricular terms to annotate the data in Fig 8, right?

David

Original comment by: ukemi

[gocentral]

Hi David

looking at this paper again I am not totally convinced that they use ventricular cardiomyocytes in figure 8, they use ventricular cardiomyocytes in their electron microscopy but they don't actually state ventricular in the methods or fig legend for these cells. But they could easily have forgotten to include this information.

The term genie terms I created were: GO:1900827 positive regulation of membrane depolarization involved in regulation of cardiac muscle cell action potential GO:1900825 regulation of membrane depolarization involved in regulation of cardiac muscle cell action potential GO:1900826 negative regulation of membrane depolarization involved in regulation of cardiac muscle cell action potential

These have now been used to annotated several proteins so I guess they are staying

Ruth

Original comment by: RLovering

[gocentral]

• status: open --> closed-accepted

Original comment by: ukemi