The UCSC University of California Santa Cruz Genome Browser the golden path genome'ucsc'edu

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The UCSC (University of California Santa Cruz)
Genome Browserthe golden pathgenome.ucsc.edu

• Stephen Baird
• Apoptosis Research Centre
• Childrens Hospital of Eastern Ontario
• sbaird_at_arc.cheo.ca

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Jim Kent

• First assembly of the human genome as a graduate
  student with his program GigAssembler

• Catalog of software includes
• blat - Fast alignment of similar sequences.
• autoSql - create SQL and C code for permanently
  storing a structure in database and loading it
  back into memory based on a specification file
• ameme - Find motifs in DNA sequence.
• 40 other command line programs for genome browser
• The Intronerator - to look at C. elegans genes
  and splicing patterns.
• cis-Site Seeker - Look for regulatory regions in
  RNA or DNA sequences

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UCSC Genome Gateway Structure
Custom tracks
Genome browser
Table browser
Your sequence
Gene sorter
BLAT
in silico PCR
Proteome browser
Downloadable data files
Public MySQL server
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The UCSC Home page genome.ucsc.edu
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UCSC Genome Browser Gateway- start page, basic
search
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Overview of the whole Genome Browser page

Genome viewer section
Groups of data
Variation and Repeats
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Configure Tracks Spliced ESTs, Microarray
Expression, Repeats, etc
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Spliced ESTs By UCSC
Simple Repeats
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Known Gene Details page for Clock gene
Gene Description
Links to Tools/DBs
UniProt Description
Links to output Sequence
Microarray data
mRNA secondary structure
Protein domains/structure
Homologs
Gene Ontology (GO)
mRNA descriptions
pathways
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Proteome Browser
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Genome Gateway Help/Users Guide
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BLAT Blast Like Alignment Tool
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In Silico PCR
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Gene Sorter and Table Browser

• Query database by filtering and cross references
  all of the data tables of the database to output
  sequence, genomic positions or text data.
• What are in all the tables?
• genome.ucsc.edu/goldenPath/gbdDescriptions.html

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Gene Sorter

• display a sorted table of genes that are related
  to one another

• EXAMPLE 1 Make a list of genes of membrane
  proteins that are highly expressed in pancreatic
  islet cells to possibly explore the role of
  autoimmunity in Type 1 Diabetes.

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Gene Sorter - Configure
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Gene Sorter - Filter
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Gene Sorter - Output
Sequence- genomic, protein or mRNA
Text Tab delimited
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Gene Sorter - To Try Now

• EXAMPLE 2 Find genes expressed predominately in
  the mouse adrenal gland that have human
  homologs. Get the sequence data and examine
  the expression of the human orthologs.

• Enter any gene to start.
• In configure menu (a) Expand tissue selection of
  GNF Atlas 2 to median of replicas, (b) click on
  human homologs
• In filter menu (a) set adrenal gland minimum box
  to 2.5, (b) look at results and set maximum box
  of other commonly expressed tissues to 0.5
• Complete solution in notes 7.2 UCSC.

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Table Browser
Groups as in Browser
Tracks within Group
Filter fields in Table and connecting Tables
Intersect non-connecting Tables by position
RESET!
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Table Browser table schema
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Table Browser Example

• EXAMPLE 3 Find CpG islands in known genes on the
  last part of chromosome 22 of the human genome.
  Obtain the genes sequences as one fasta record
  per region.

Change to
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Table Browser CpG Example
Set group for Expression and Regulation and
track for CpG Islands
Click on intersection
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Table Browser CpG Example
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Table Browser CpG Example
Copy and paste sequences or Set up an output
file in the Table Browser
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Table Browser Example To Try

• EXAMPLE 4 Find trinucleotide repeats of more
  than 10 copies within mRNA sequence on human
  chromosome 4. How many are there? How many are
  linked to known disease genes?

• Hints
• Period 3, copies gt 10.
• Intersect tables and custom track.
• Tables knownGene, simpleRepeats, spDisease

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VisiGene-in situ mRNA and protein images in mice
and frogs
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Data Downloads- from download link on homepage
. . .
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Example simpleRepeats table
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Public MySQL Server

• See the Data and Downloads FAQ
• Direct MySQL access to data
• http//genome.ucsc.edu/FAQ/FAQdownloadsdownload29
  
• Command from local MySQL client
• mysql --usergenome --hostgenome-mysql.cse.ucsc.e
  du -A