Genome Browsers

We are going to look at two public genome browsers:
  1. EBI's Ensembl
  2. the UCSC Genome Browser (European mirror)

Exercises:

  1. Are there any vertebrates that are only found in one of the two browsers?
  2. Looking for the human HBB gene (hemoglobin, beta) in the UCSC browser will bring up a 1,606 bp region (UCSC Genes track). Searching for HBB in Ensembl leads to a region nearly 4 kb in size. Can you explain the difference?
  3. Try to find out which tissue the following genes are mostly expressed in. Compare results between the two browsers:
    SPATA19
    SPP2
    XP32
    RHO
    
  4. Here is an excerpt from a paper on blue eye color in humans:
    "In total, all these data strongly suport a model where the blue
    eye color in humans is caused by homozygosity of the
    rs12913832*G allele."
    
    Find out which of the resequenced individuals (available in Feb 2014 archive) might have blue eyes. Can you confirm your findings through a Google image search?
  5. See Eupedia for a list of addiction-related SNPs. Which individuals might be at risk of nicotine/cocaine/cannabis dependence?
  6. Select the 2006 version of the fruit fly (dm3) in UCSC and upload a custom track in BED format (URL: http://bioinf.gen.tcd.ie/GE3M25/bioinformatics/Weederh_and_RedFly.bed) with TFBS predictions from WeederH and experimentally verified TFBSs from the RedFly database. How do they match up with conserved regions and ChIP peaks?



kahokamp@tcd.ie