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Homework for Lesson 5: Genome Browsers
The assignment is for you to explore thoroughly a genome browser of interest to you. If you are
interested in genomes that are well-supported at UCSC and Ensembl, which includes genomes
of most vertebrates, then use UCSC or Ensembl. As you noticed, I have emphasized the UCSC
Genome Browser because of its versatility, near-ubiquity in analyses of vertebrate genomes,
and its organization around genome assemblies. However, if you are studying other types of
organisms (microbes, flies, worms, Arabidopsis, etc.) this is a good opportunity to delve into the
most relevant databases. The user interfaces are distinctive for each, although there are many
general similarities.
Please turn in a report about what you learned in your exploration. A page should be sufficient.
The main aim is for you to work from the information in the assigned paper (Kuhn et al.) and
presentation and develop some expertise with genome browsers. Explore the “track search” tool
for finding particular types of data – or the Table Browser – or just examine the listed tracks.
For those who want a specific goal, start at the the ANK1 gene (human hg19), and find out
some specific information, such as:
1. What are the neighoring genes?
2. Is there evidence for alternative splicing for ANK1?
3. What tissues is it expressed in?
4. Are there noncoding transcripts in the locus?
5. Are there microRNAs in the locus?
These are just suggestions – follow your own interest and curiousity.
For those who want more general guidance, here is some advice. As you explore the
functionality of the genome browser(s) you chose, you may want to keep in mind questions ike
the following:
How complete is the genome sequence assembly?
Where are the protein coding genes? How do I find ones that I’m interested in?
What regions are transcribed? In what tissues are they transcribed?
Where are the gene regulatory regions? Are there cis-regulatory modules outside the promoter
regions?
Is there information about the chromatin that packages the DNA?
Is there information about genetic variants within the species?
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