Gene not found in Affymetrix expression profiles

Question

[lorenzo_fabbri]

I am studying the ABA network in A. thaliana, consisting of HB7, ABI1 and AREB2. The AGI code I was given are, respectively: AT2G46680, AT4G26080 and AT1G45249.

I downloaded the following file (https://www.arabidopsis.org/download_files/Microarrays/Affymetrix/affy_ATH1_array_elements-2010-12-20.txt) in order to convert the array element name to the AGI one, but I am not able to find AT1G45249 in the above file. How can I check whether AT1G45249 has another name? Or even better, how can I check what is the array element name in Affymetrix (GPL198) corresponding to AT1G45249. Thank you.

[afli]

Hi, microarray datas have a limit gene number predicted from the reference genome. If you want to investigate all the gene expreesion, you may download some RNA-seq data from NCBI in A.thaliana, there must be a lot of data.

Answer 1

[h.mon]

According to the Affymetrix Probe Set ID found at the GEO site, neither the gene AREB2 nor the AGI AT1G45249 are part of the array. However, according to TAIR, AREB2 is a synonymous of AT3G19290, which is found on the array.

[lorenzo_fabbri]

Thanks a lot, I suspected that but needed confirmation!