collect data on host cell localization

[andrewsu]

doesn't have to be complete, just enough example cases to show in paper.

[andrewsu]

kevin will provide a list of genes that localize to inclusion membrane

The list of all possible localizations can come from the SVG -- @putmantime and I need to find closest mappings in GO (and request new terms if necessary)....

[khybiske]

Done! I tabulated all of the relevant genes: google sheet

[andrewsu]

@khybiske three questions for you...

First, you annotated CT456 / CTL0716 / TC0741 to "actin cytoskeleton". I just want to confirm that you mean the chlamydia actin cytoskeleton and not the host actin skeleton, correct?

Second, just to be sure we get it right, can you highlight/describe exactly what should be colored for "inclusion membrane"? Is it the outer ring of the shaded circles? Just trying to differentiate it from "EB" component.

Third (and this one might be the toughest), if we are going to add these annotations to Wikidata, then ideally we need a reference to support the localization annotation. Also we ideally need to know which exact protein was mentioned in the reference (on the assumption that only one of these CT005 / CTL0260 / TC0273 was actually studied, and the other two were inferred based on their sequence similarity). How difficult would it be to add those to the spreadsheet? Again, even doing just a handful of cases would be just fine...

[khybiske]

@andrewsu

1. I actually do mean the host actin cytoskeleton (the straw like stuff close to the plasma membrane). I chose this CT example as one that we know is secreted into the host cell. Annotating proteins like this (CT has ~100 of them) is pure magic if we can capture that.

2. Inclusion membrane = the nucleus-size membrane encircling all of the bacteria. I made 2 sizes of bacteria, EB (shaded dots) and RB (larger circles). A 4th compartment would be the white inside of the inclusion. We have some data (from literature, not in NCBI etc) which I can annotate into all 4 of these locations.

3. Not that difficult actually. If you send along whatever master sheet you'd like me to use, I can easily populate it with 40+ evidence-based examples. Nothing I would annotate would be from pure speculation or prediction.

[andrewsu]

great, thanks!

1. I updated the google spreadsheet to say "host actin cytoskeleton".

2. Super, very clear now, thanks. I think annotating at least one example gene for each of those four compartments would be great actually...

3. Great, let's use the same google sheet that you prepared. I added two columns for "PMID of supporting paper" and "Specific Gene ID studied in paper". No need to fill those out for every row in the sheet -- just enough for a representative example.

[khybiske]

@andrewsu 'Specific Gene ID' = what exactly? NCBI #?

[andrewsu]

@khybiske I would say any of the gene symbols from columns A-C, e.g., CT005, CTL0260, or TC0273. I changed "gene ID" to "gene symbol" in the header to hopefully make that clearer...

[khybiske]

@andrewsu I'll get this done by tomorrow. Is Derek working on the implementation?

[andrewsu]

yes, Derek is on it! He's remapping the SVG to the "host" versions of the GO terms. Once you get more info on host cell localization, we'll add that to wikidata and then everything should just automagically work. 🤞

[khybiske]

@andrewsu Sheet is done!

[andrewsu]

looks like we have all the data we need, so closing this issue