Difference Between Gene Expression And Transcript Expression

Question

[jack]

What is the difference between gene expression and transcript expression ? for me both of them seems same.

Answer 1

[Floris Brenk]

Genes can have multiple transcripts. So gene expression could mean the overal expression of all transcripts of a gene. Transcript expression is the expression of a specific transcript. In the past microarray period gene expression was measured and the output was gene expression. Nowadays with next gen sequencing methods like RNA-seq, CAGE etc. specific transcript expression can be identified... Maybe read a bit about alternative splicing (http://en.wikipedia.org/wiki/Alternative_splicing)

[ammar.husami]

to add: depending on how the gene is transcribed you get multiple alternative mRNA transcripts. Some transcripts are longer or shorter by one or more exons. Some mRNA transcripts further get spliced to be modified. Some transcripts could be expressed (translated) into mature proteins in specific tissue types and become dominant (http://www.ncbi.nlm.nih.gov/pubmed/8449945)

Answer 2

[Neilfws]

In a sense, there is no such thing as a gene. A gene is a concept: a fuzzy bounded region of a chromosome within which transcription occurs. So really there is no gene expression, only transcript expression.

I'd even argue that "expression" itself is not a very useful term and we should simply use "transcription".

Answer 3

[Emily]

It may also depend on the tools you're using. You may be able to determine that there is expression from a particular gene, but the tool you're using may not be able to differentiate between alternative splicing - in this case I would talk about gene expression. If I had more accurate tools, however, I might talk about transcript expression.

Eg, an RT-PCR using primers that both fall in the middle of a large constituent exon would give us info on gene expression. An RT-PCR using primers that spanned an intron junction that was specific one splice variant would give us info on transcript expression.

[caro-ca]

Does VEP detect alternative splicing? I am asking because I have used VEP for three experiments and in all of them I got the same number of genes and transcripts where the TE variant overlapped. Thank you for your help.

Ensemble #VEP