Dear all, 

considering a RNA-seq experiment and analysis that provides the expression values as TPM, please would you let me know what is a minimum TPM value in order to consider a gene to be expressed ?

talking about RPKM.FPKM units, I remember that a gene was considered expressed if RPKM (or FPKM) > 1 ... thanks a lot, 

-- bogdan
I do not believe there is any definitive answer. There are so many factors that go into each experiment such that it is difficult to pick a value. A RPKM / FPKM value of 1 seems quite low to me, i.e., in 'error' territory. What you have to consider is the distribution of your data and the suitability of it for whatever downstream tools you will use. If including low-count / low expressed genes is going to distort your data distribution and introduce biases, then you need to remove them - check via histograms.

From RNA-seq, most genes are lowly expressed, possibly due to transcriptional 'noise' more than anything else. I say 'noise' in the knowing that they may reflect genuine transcription but have no regulatory function and are artifacts of other transcriptional processes that have occurred. They may also reflect regions where TF binding and/or promoter activity was weak.

So, you have the liberty to choose your own cut-off for TPM and state it in the methods. :)

Please take the time to read Gordon's answer, here: https://support.bioconductor.org/p/98820/#98875

Kevin

Edit: another interesting discussion: https://www.researchgate.net/post/How_to_determine_whether_a_gene_is_expressed_in_RNA-seq2