Question: single probe represent multiple genes?

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Vinay Baranwal

Hello Mathavan,

This problem is due to biology. Duplicated genes, regions etc are regions from where probes have been selected. Even this issue remains in case of NGS as well.

The way we use to tackle it in the case of rice is making a unique list of genes. We define certain criteria and stick to it throughout the analysis. Like for example selecting those probes to genes IDs which have highest expression.

Pawel Buczkowicz

Hi Mathavan,

If you are asking about this particular case, it can be explained by the fact that INO80B and WBP1 genes can sometimes occur as a read-through transcript that cannot be distinguished from either of the genes individually by the probes in question (see https://genome.ucsc.edu/cgi-bin/hgc?hgsid=579057461_Tm25CaPexEPPpKrMhRyrGSqaNmCR&c=chr2&l=74456725&r=74462493&o=74455022&t=74460891&g=refGene&i=NR_037849).

You can also look up more information about the U133 array's probes sensitivity and specificity to certain transcripts to understand why this could be for other probes and genes. For this particular example you can look at the information for probe 65133_i_at here https://genecards.weizmann.ac.il/cgi-bin/geneannot/GA_search.pl?keyword_type=probe_set_id&array=HG-U95&target=genecards&keyword=65133_i_at and for the 223072_s_at probe see https://genecards.weizmann.ac.il/cgi-bin/geneannot/GA_search.pl?keyword_type=probe_set_id&array=HG-U133&target=genecards&keyword=223072_s_at.