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Post by DAVID user on Jul 20, 2020 14:22:44 GMT -5
Hi there,
Is there a way to query which species are in the DAVID knowledgebase?
The content page only says that the DAVID 6.8 annotation sources have last been updated in May 2016.
One of my study systems is Epichloƫ (Clavicipitaceae). Specifically, I have gene models for E. amarillans and E. elymi.
I know I will need to generate a list of orthologs with gene identifiers of a format recognised by DAVID, as my current gene models only have in-lab identifiers.
I've tried submitting some random refseq mRNA gene IDs of Pochonia chlamydosporia (Clavicipitaceae) to DAVID, just to see whether those will produce a result
XM_022430235
XM_022430234
XM_022430233
XM_022430232
XM_022430231
, but the screen that follows prompts me to either convert the gene list or go back to the submission form.
Does that mean DAVID doesn't contain annotations for that species?
How would one go about deciding which species to use to generate that list of orthologous genes to ultimately be used in DAVID?
Would greatly appreciate your help with this again.
Many thanks,
Anna
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Post by Brad Sherman on Jul 20, 2020 14:25:51 GMT -5
Hi Anna, Unfortunately, there is no mechanism at this time for users to directly get that information. You could register/login and download parts of the knowledgebase for your species at david.ncifcrf.gov/knowledgebase/login.html and we are happy to provide you the information as well. Perhaps this can be a future feature. Currently, there are 14,980 genes listed in our production knowledgebase for Pochonia chlamydosporia 170 (species based on XM_022430235) with 14,867 of these mapping to refseq mrna ids in the knowledgebase. It's not quite apparent why your example ids are not in the production knowledgebase but I do see them in the update that we are working on currently. How are you performing the conversion from the in-lab identifiers? Regards, Brad
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Post by DAVID user on Jul 20, 2020 14:29:23 GMT -5
Hi Brad,
Thanks very much for your response.
I'm performing the conversion from my in-lab identifiers using proteinortho. So far I've generated a list of Metarhizium robertsii orthologs for my Epichloe amarillans gene models. eg: XM_007819910 XM_007822631 XM_007819918 XM_007821711 XM_007822639 XM_007819916 XM_007826445 XM_007826444 XM_007821708 XM_007819996 XM_007822633 XM_007821963 XM_007821964 XM_007818730 XM_007818729
I have created a login for the knowledgebase, and have been searching through there, though I'm not sure if I'm accessing it correctly. For instance, if I search for Metarhizium robertsii in the knowledgebase request form, it doesn't appear to have that species in the database. However, running the above list of refseq mRNA IDs in DAVID, does produce annotation results.
When I searched for Pochonia chlamydosporia, refseq mRNA (GOTERM_BP_ALL GOTERM_CC_ALL GOTERM_MF_ALL) in the knowledgebase request form, I then received an email that refseq mRNA was not available for that species.
So I'm not sure what I have done wrong there.
I also couldn't find the option in the knowledgebase request form to request KEGG pathway annotation, in general.
Would you please be able to tell me if you have refseq mRNA IDs for: -Squalius pyrenaicus (or S. alburnoides, or any other Squalius species if pyrenaicus is not available) -Epichloe amarillans (or any Epichloe species if amarillans is not available) -Metarhizium robertsii
and if so, how many?
I hope that's not too much to ask; querying any species within a genus instead of a specific one.
Thank you so much for your time.
Regards, Anna
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Post by DAVID user on Jul 21, 2020 14:20:29 GMT -5
i Anna, Thank you for the information. Please see the counts for DAVID genes and refseq mRNAs for your requested species below. It seems that the production knowledgebase does not have data for Squalius and Epichloe species at this time. Pochonia chlamydosporia 170 and Metarhizium robertsii ARSEF 23 seem to have the best coverage in the knowledgebase. KEGG is not available for download due to licensing restrictions. Please let us know if you have any other questions. Regards, Brad
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Post by DAVID user on Jul 21, 2020 14:21:34 GMT -5
Hi Brad,
Thank you very much for that -- very appreciated.
Kind regards, Anna
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