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Exercises for UCSC Advanced Topics:
Table Browser and Custom Tracks
1) Obtain a list of SNPs in a single gene (Clock) using the Table Browser.
Skills: basic table search menus and options; choosing format; downloading sequence
2) Find CpG islands in known genes on the last part of chromosome 22 of the human
genome. Obtain this sequence as one FASTA record per region.
Skills: basic table search menus and options; intersecting tables, choosing format, downloading
sequence
3) From a list of UCSC genes, add gene symbols and GO IDs for additional information
about the gene set. Bonus step: add GO terms.
Skills: basic table search menus and options; using tables, choosing related tables and selected fields
UCSC Advanced Topics Exercises, version 15b.
Correspond to the data available in October 2008.
The materials and slides offered are for non-commercial use only. Reproduction, distribution
and/or use for commercial purposes are strictly prohibited.
Copyright 2008, OpenHelix, LLC.
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Step-by-Step instructions for the UCSC Genome Browser
Advanced Topics exercises
1) Obtain a list of SNPs in a single gene (Clock) using the Table Browser.
Step Action
1 Go to the UCSC Genome Browser homepage, genome.ucsc.edu.
2 Enter the Table Browser, by clicking either of the Table Browser links
from the homepage.
3 Choose “human” and the “May 2004” assembly.
4 Choose a table: Choose group “Variation and Repeats” in the “group”
pull-down menu, “SNPs’ in the “track” menu and “snp125” in the
“table” menu.
5 Type in “CLOCK” in the position box.
6 Click the “lookup” button.
7 You will see a list of records with “Clock” in the record. Click the first
link “CLOCK (NM_004898)”. The position of this gene will appear in
position box. (Alternatively, you could paste in a known accession
number and choose that option, but we wanted to show how the ‘look
up’ works here.). This should give you the position: chr4:56139588-
56253925.
8 Leave buttons for filter and intersection as default (none).
9 Under “Output Format” choose “selected fields from primary and
related tables” in pull-down menu. Click “get output.”
10 In the resulting menu, check the boxes for these fields: chrom,
chromStart, chromEnd, name, strand, observed and func. Click
“get output.”
11 You can now copy/paste or download the resulting file for more study.
Clock is an interesting gene that encodes a protein associated with
circadian rhythm sleep disorders.
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2) Find CpG islands in known genes on the last part of chromosome 22 of the human
genome. Obtain this sequence as one FASTA record per region.
Step Action
1 Go to the UCSC Genome Browser homepage, genome.ucsc.edu.
2 Enter the Table Browser, by clicking either of the Table Browser links
from the homepage.
3 Choose “human” and the “May 2004” assembly.
4 Choose a table: Choose “Genes and Gene Predictions Tracks” in
“group” pull-down menu, choose “Known genes” in the “track” menu
and “knownGene in the “table” menu.
5 Type in “chr22:40000000-49396972” in the position box.
6 Click the intersection “create” button.
7 On the resulting page, choose “Regulation” in the group menu and “CpG
Islands” in the track menu. Leave other options as default (“all Known
Genes records that have any overlap with CpG Islands”) and click
submit.
8 On the resulting page (back to table browser interface), choose
“sequence” on the output format menu. Click “Get Output.”
9 On resulting screen, choose “genomic’ and click submit.
10 Make sure only “5' UTR Exons, CDS Exons, 3' UTR Exons” options are
chosen (unclick introns). Then click on the One FASTA record per
region option and leave rest of the sequence retrieval options as default.
Click “Get Sequence.”
11 You can now copy/paste or download the resulting file (a list of CpG
islands in known genes) for more study. The resulting file will be large. In
cases like this, it is best to type in a file name in the “Output File” box.
This will save a FASTA formatted text file to your computer.
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3) From a list of UCSC genes, add gene symbols and GO IDs for additional information
about the gene set. Bonus step: add GO terms.
Step Action
1 Go to the UCSC Genome Browser homepage, genome.ucsc.edu. Enter the
Table Browser by clicking either of the homepage Table Browser links.
2 Choose “human” and the “Mar 2006” assembly.
3 Choose “Genes and Gene Prediction Tracks” group and the track
“UCSC Genes.” The table you will need first is “knownGene”.
Note: For this exercise and similar searches, it is useful to know which tables
contain the data you need. If you choose the table and click the “describe
table schema” button to examine the data fields within. This will also list all
the tables linked to this table and joining fields.
4 Choose the “position” radio button and type chr7 as the location. Click
“lookup” to add the nucleotide range quickly. This just limits our set of data
for this example. You can choose genome-wide, if that’s what you need, later.
5 Leave all other choices as default and choose “selected fields from
primary and related tables” in the “output format” menu.
6 Click “get output.”
7 On the next page you choose the items available for the output. At the top is
our table choice. Select “name” and “chrom” and “proteinID” for our
purposes. You may find other times you want more data.
8 We now need to add data from linked tables. In the lower area, select one
table from which we need data, by clicking the checkbox: “kgXref” (a
cross-reference table for various identifiers). Now click “Allow Selection
from Checked Tables” at the bottom of the page to view choices for table.
9 In hg18.kgXref fields box, choose “kgID,” “geneSymbol” & “refseq”
fields.
10 By making the kgXref table available, new associated tables are now also
available from the “Linked Tables” area below. One of the new choices is go.
Click the checkbox next to go for the “goaPart” table. Click “Allow
Selection from Checked Tables” to view the choices for that table.
11 In the new table box “go.goaPart Fields,” select the field “goId.”
12 Click “get output” in the box “Select Fields from hg18.knownGene” in the
top section of the page. Your results will display UCSC IDs, chromosome,
protein ID, GO IDs, and gene symbols, which we built from the series of table
choices.
13 Extra credit: return to the last checkbox page and add GO terms by checking
the other “go” box (“term”) in the “Linked Tables” area. Then check
“Allow Selection from Checked Tables,” and add “name” from go.term
fields. Get output.