Contents
- 1 What is transcript expression?
- 2 What’s the difference between intron and exon?
- 3 Is isoform the same as transcript?
- 4 How are gene counts and constituent transcript counts plotted?
- 5 How is gene-level differential analysis similar to transcript analysis?
- 6 How are transcript counts converted to p values?
What is transcript expression?
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).
What’s the difference between intron and exon?
Introns and exons are nucleotide sequences within a gene. Introns are removed by RNA splicing as RNA matures, meaning that they are not expressed in the final messenger RNA (mRNA) product, while exons go on to be covalently bonded to one another in order to create mature mRNA.
What is a gene length?
A gene’s length—defined as the number of bases in the primary transcript prior to splicing—ranges over four orders of magnitude in the human genome (Fig. 1A). We asked whether the previously reported inverse relationship between alternative splicing and gene duplication (Kopelman et al.
Is isoform the same as transcript?
An isoform is specifically one of many splice variants of a gene, while a transcript is an expressed sequence. The difference is that “isoform” implies that there are multiple isoforms, while transcript makes no such implication.
How are gene counts and constituent transcript counts plotted?
Gene counts and constituent transcript counts are plotted between conditions (dexamethasone vs vehicle treatment) and annotated with Ensembl ID and sleuth-derived p values. In the case of cancellation ( a ), the abundance of transcripts changing in opposite directions cancels out upon conversion to gene abundance.
How are transcript counts proportional to transcript length?
Because transcript counts are proportional to transcript lengths, summing transcript counts is not equivalent to summing transcript abundances.
How is gene-level differential analysis similar to transcript analysis?
Gene-level RNA-seq differential analysis is, at first glance, similar to transcript-level analysis, with the caveat that transcript counts are first summed to obtain gene counts [ 4, 5 ]. However, despite such superficial simplicity, there is considerable complexity involved in transitioning from transcripts to genes.
How are transcript counts converted to p values?
The x -axis is labeled with the Ensembl gene and transcript IDs, along with p values obtained by performing sleuth on transcripts and genes. In this process, the transcript counts ( a) are converted into transcript abundances ( b) by normalization according to transcript lengths.
https://www.youtube.com/watch?v=Nm4QY3_5Ts0