Saturday, November 9, 2013

v27 (1 of 3): GENCODE V17 track for the human genome

GENCODE version 17 of the human genes are now on hg19. Credit goes to UCSC Genome Browser where the data was obtained. GENCODE is one of the most finely curated gene tracks out there, and we're really happy to have it in our Browser.

http://epigenomegateway.wustl.edu/browser/?genome=hg19&gftk=gencodeV17,full







Genes are assigned into 5 categories, distinguished by color:

      coding genes
      non-coding genes
      pseudogenes
      with problem!
      polyA signal

For the "problem" ones, their causes can be seen in the tooltip bubble, such as "retained_intron".

In the tooltip, links are given to the gene model's record in GENCODE database.



This is the start of the effort to improve all the gene tracks on our Browser, including the underlying mechanism. Right now the GENCODE V17 track is new format and is supported by new mechanism, alongside the old gene tracks such as refGene, GENCODE V11.

With the new mechanism we can reduce the dependence on mysql storage and store all the data in the compressed track file, so that the new gene tracks can work as custom tracks. On such basis a new track type is been developed to support the RNA-seq experiments.