Do gene expression microarrays cover all genes in the transcriptome?

Question

[Volka]

Hi all, as title says, I have been reading on gene expression and microarrays and I am wondering if all the probesets on the microarray cover all the genes? For example, does the Affymetrix Human Gene ST arrays cover all human genes?

[arta]

If you aim to detect something new, you can not do that using microarray since it is array (probe) based technology. Even if, you know the sequence and design a probe to capture the sequence, it is not guarantee that you will detect it due to very low and high expression of the sequence. Microarray was replaced by RNA-seq which has more advantages than microarray.

[Volka]

Thanks for the reply. Does that mean that microarrays are limited by genes that are known? Do they do a good job of probing for all of these known genes?

[arta]

Does that mean that microarrays are limited by genes that are known?

Yes.

Do they do a good job of probing for all of these known genes?

Yes, they design probe for all known genes. But there are limitation of detection as i said before. You can read that paper where they compare microarray to RNA-seq.

[Kevin Blighe]

The latest microarray releases are comprehensive, though, and target the majority of the >200,000 transcripts (inclding their isoforms) identified by the ENCODE project. Not just that, microarray releases also target annotation listed in other projects, such as VEGA genes. Further information: Micro array VS RNA seq