For example Cit.9890.1.S1_s_at is 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.
mapping a list of affy IDs from citrus to arabidopsis locus IDs
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
2 answers
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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