Transcripts per kilobase million

Question

[mrashad]

While using GTEx portal to find out tissue specificity of certain genes, I found that median TPM of these genes = zero, I just need to ask if the median TSM of certain gene in certain human tissue = zero, this means that the gene is not found in this human tissue or maybe it is found but not expressed. If there is an easy resource to let me understand this issue, please provide me.

Answer 1

[i.sudbery]

The median is the value at which half of samples have the same or lower value.

If the median TPM of a gene is zero, then that means that at least half of samples have a TPM of 0.

This means that in at least half of samples none of the reads in the sequence run mapped to that gene. It does not tell you anything about how many reads were found in the other 50% of samples.

Further, a TPM of 0 just tells you that no reads were recovered, not necessarily that the gene is not expressed. It could, for example, be expressed, but at a sufficiently low level that no reads were recovered.