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?