Difference Between Gene Expression And Transcript Expression

Question

[mkh]

Hi All,

I know there is a discussion regarding difference between gene and transcript expression at BioStar. However, I am still confused and I would like to open this discussion again. I have a RNA-seq data (analyzed by kallisto/Sleuth) which shows significant changes in gene expression at transcript level but not at genes level. In other word, e.g. gene x is significantly and highly expressed at transcript-RA but not transcript-RB or transcript-RC. When I looked at the gene expression of gene x at gene level the expression is low and not significant. So, my question is how the gene expression considered? (I thought the gene expression is a sum of transcripts expression of gene x, but based on my observation it is not!). How gene expression computed at gene level?

Thanks Morteza

[h.mon]

It depends on how you did your transcript- to gene-level summarization, which you didn't tell us how you performed. I am not familiar with kallisto and Sleuth, do they provide some method or function to do such summarization? I am aware of tximport, in which case I believe gene-level should be (approximately) the sum of the estimated counts for all transcripts from that gene.

[t2g4free]

I think the biggest question is how to decide the same exon belongs to different transcript. Then you will got it. Hope helpful.

[h.mon]

kallisto uses an EM algorithm to distribute reads along different transcripts sharing exons.