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The central dogma of gene expression includes two sequential steps: transcription (DNA to RNA) and translation (RNA to protein). Transcription is the key step that controls the ?on and off? of genes and subsequently underlines the identity and the status of the cell (Young, 2011; Lee and Young, 2013).

Expression of a transcript is proportional to the number of reads sequenced from that transcript after normalizing for that transcript's length.

A transcriptome represents that small percentage of the genetic code that is transcribed into RNA molecules ? estimated to be less than 5% of the genome in humans (Frith et al., 2005). The proportion of transcribed sequences that are non-protein-coding appears to be greater in more complex organisms.

Transcript expression level, refers to how abundant a transcript is, i.e. if a certain mRNA (a transcript) exist in many or few copies (expression level). DE analysis is the analysis of Differentially Expressed genes.

Differential transcript expression (DTE) refers to change in one of the isoforms. Differential gene expression (DGE) refers to change in overall gene expression (i.e. expression as the sum of the expression of the two isoforms).

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