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
As already pointed out, there is no ideal cutoff. However, there is at least one method, zFPKM, that tries to define an expression cutoff.

BioC: https://bioconductor.org/packages/release/bioc/vignettes/zFPKM/inst/doc/zFPKM.html

Publication: https://www.ncbi.nlm.nih.gov/pubmed/24215113

> the community adopted several heuristics for RNA-seq
> analysis, most notably an arbitrary expression threshold of 0.3 - 1
> FPKM for downstream analysis. However, advances in RNA-seq library
> preparation, sequencing technology, and informatic analysis have
> addressed many of the systemic sources of uncertainty and undermined
> the assumptions that drove the adoption of these heuristics. ... We
> use ENCODE data on chromatin state to show that ultralow-expression
> genes are predominantly associated with repressed chromatin; we
> provide a novel normalization metric, zFPKM, that identifies the
> threshold between active and background gene expression; and we show
> that this threshold is robust to experimental and analytical
> variations.

