Nomenclature: Genes With Reads In An Rna-Seq Experiment?

Question

[14134125465346445]

I would like to know what is the best way to call the set of genes that show "at least one read" in an RNA-seq experiment. This is, those genes that have at least one read mapping to their exonic body. There are papers out there that have split these in two classes: those genes that show reads in RNA-seq but lowly-expressed, and the highly-expressed genes: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159973/

What is the best term to call all genes with reads present in the RNA-seq experiment? Maybe "expressed genes"? Or "ascertained genes"? Or "assayed genes"?

[Sebastian Kurscheid]

Interesting question. I suppose it could be debatable if a single read mapping to any position of a gene's exonic body is enough evidence of active gene expression. If you want to hedge your bet you could perhaps call them "transcribed genes".

[Istvan Albert]

There is also the open question of how many reads should be matching to the gene for it to be called even lowly expressed. For that it should be above some sort of background.

For example taking a single read is almost certainly not enough to characterize the gene as anything other than an annotated region with at least one read matching

[David Langenberger]

I think it also depends on the length of the read. I would trust one long 454 read much more than three short illumina reads.

Answer 1

[seidel]

"Detected" seems the most straightforward to me. With one read, one can consider something detected, at least versus zero reads. While most would agree that certainty is in question, and you'd have to cite that one read was the definition of detected. Nonetheless, I think it's the simplest and most descriptive relative to the other terms you suggested. "Expressed", "ascertained", and "assayed" all have an extra layer of meaning that I think you'd want to avoid with only a single read.