Travel through Transcript evolution with the Gencode version Time Machine in R2platform

The definition of genes and transcripts contained within these bounderies is by no means fixed. As a scientific community we keep on learning, resolving and discovering adaptations on our gene models.

The Gencodegenes consortium forms a rich resource that keeps us up to speed with the recent developments in our understanding and composition of transcripts. They do this with version controlled updates that occur a few times per year.

Within the embedded Genome Browser of the R2 genomics analysis and visualization platform ( https://r2.amc.nl ), we also maintain a Gencode version Time Machine track. This track allows you to easily grasp how some transcripts are very stable, and have not changed at all, while others are still changing from gencode version to version.

Within R2 we also publicly provide the RNA Atlas, which is a comprehensive collection of deeply profiled ~300 tissues, cell types and cancer cell lines, all assessed by polyA as well as total RNA sequencing. This rich resource serves as a perfect reference for RNA expression as a whole. Things can really become interesting by combining those 2 resources, giving us a comprehensive view on both 'transcription', as well as 'transcript models'.

By simply using a cutoff on the expression signal, you can then see where certain transcript isoforms may yield an appreciable level

You can explore the whole genome in the R2 platform ( https://r2.amc.nl ) both from the perspective of the Gencode version Time Machine perspective ( in hg38 of the genome browser ), as well as from the RNA Atlas perspective, the latter of which we have a whole publicly accessible DataScope ( http://r2platform.com/rna_atlas ) for in the platform.

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