canned query Proteins conserved in human/vertebrates
Closed this issue · 14 comments
This list is vertebrates and contains 3 genes that are conserved to metazoa but absent from humans (related to amino acid biosynthesis).
I used to think this was OK, but instead can we make this query reflect proteins with annotated human orthologs (also I think it has a couple of RNAs too)
Can you make the query you'd like in the query builder and then send me the link?
I don't think we can do this in the query builder.
We could only do it if we were able to query "genes with human orthologs" and we can't do that query.
The "vertebrates" list has
SPBC1A4.02c | leu1 | 3-isopropylmalate dehydrogenase Leu1
SPBC405.01 | ade1 | phosphoribosylamine-glycine ligase/phosphoribosylformylglycinamidine cyclo-ligase
SPCC569.08c | ade5 | phosphoribosylglycinamide formyltransferase
SPAC23H3.09c | gly1 | threonine aldolase Gly1
that are in vertebrates (some even in mouse) but not human
It would be good if there could be some way to engineer the precise human query.
This isn't super urgent but we should keep it on the radar
We could only do it if we were able to query "genes with human orthologs" and we can't do that query.
We can do that in the query builder:
OK we should use that for the canned query!
I had got so used to using the canned query I forgot about this.
We should also update this FAQ!
https://www.pombase.org/faq/how-can-i-find-all-s.-pombe-genes-are-conserved-human
which explains that the query has a couple of proteins without human orthologs (now 3 I think!)
Should the new query be named "Proteins with human orthologs" or "Proteins conserved in human"?
The cerevisiae query is a bit complicated. Should we change it to be an ortholog query too?
We should also update this FAQ!
Is this enough?:
To retreive a list of genes with a human ortholog, go to the advanced search,
click the “Commonly used queries” option and choose “Conserved in human”.
yes, the rest is out of date, that'd enough
tks
v
The cerevisiae query is a bit complicated. Should we change it to be an ortholog query too?
yes please!
The cerevisiae query is a bit complicated. Should we change it to be an ortholog query too?
The results will change a bit, mostly because of RNA orthologs:
Proteins conserved in S. cerevisiae:
https://www.pombase.org/results/from/id/2a22121d-ecb2-431b-a9f6-6ee86c20443b
has 4012
has ortholog with: S. cerevisiae:
https://www.pombase.org/results/from/id/dd028f57-6ff7-455f-ba85-fabafa5da00f
has 4042
There are 5 genes that are returned by the current "Proteins conserved in S. cerevisiae" query but which don't have a cerevisiae ortholog?:
https://www.pombase.org/results/from/id/ea94807f-77ea-4ae0-85fe-5ec17f139605
Proteins conserved in S. cerevisiae:
Should we rename that commonly used query to: "Genes conserved in S. cerevisiae" since it includes RNA genes?
Proteins conserved in S. cerevisiae:
Should we rename that commonly used query to: "Genes conserved in S. cerevisiae" since it includes RNA genes?
Or change the query so that it matches the protein coding genes (doing it the same way as the human one).
I think these canned queries were made before the ability to query on orthologs...
Or change the query so that it matches the protein coding genes (doing it the same way as the human one).
The "Proteins conserved in human" query was all orthologs, not just proteins. I've fixed that now.
I've also updated the cerevisiae and japonicus queries to also be just protein coding orthologs. It doesn't make a difference for japonicus but I wanted to be consistent.
Can we close this now?
Yes, I will check the content, but I think the remaining issues are annotation!