Hello all,
I have a list of affy IDs and gene symbol IDs, for example LOC102628104 for citrus derived from a network. How I can map these IDs to arabidopsis because IPA or pathway studio don't support all species, do you have any idea?
Thank you
Well, it seems there is no direct way to map between affy IDs and A. th loci. In Netaffx, for probes you pasted above, there are no orthologs in A.th (on A.th chip). Best way is to download annotations from affymetrix for significant affy IDs and identify the genes. Then you can cross map the genes with athaliana.
Biomart (from phytozome) also doesn't show any orthlogs between c.sinensis and Ath, with gene symbols (from Netaffx)
Btw, small request. Could you remove the long list of the probes. I saved those ($3500 probes). Keep, may be, 50 ids.
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For example
Cit.9890.1.S1_s_atis on of my affy IDs and LOC102628104 is one of the gene symbol IDs. I read somewhere I should have the fasta sequence of my affy IDs then use blast against Arabidopsis transcript to map or in another word find the equal Arabidopsis affy IDs but I could not perform this yet.I am looking for at least 10-20 affy IDs. If you have the list with you, please post IDs here. Mapping between two different genus needs good number of probes. The one you posted above is not even confirmed. It's XM.
ok thank you
thank you for paying attention to my problem...i was going to infer the pathway underlying these gene by IPA or pathway studio but they don't support citrus then i have to have the equal IDs for Arabidopsis