Transcript The Yeast Orphan Gene Project: Finding a Place for ORFans to

THE YEAST ORPHAN GENE PROJECT: FINDING A PLACE FOR
ORFANS TO “GO”
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Genomic sequence of model eukaryote Saccharomyces
cerevisiae completed in 1996. (12.1 Mb)
Despite 16 years of intense research, function of nearly
30% of putative open reading frames (ORFs) remain
unknown.
In genomics, termed “ORFans”
Likely have function specific to fungi.
Potentially important to
food and drug industry.
MODULE RESEARCH GOALS
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To determine the cellular function of a yeast ORFan gene
by:
 Reviewing basic gene information at yeastgenome.org
 Analyzing data from a comparative RNAseq analysis of
the deletion strain and the isogenic wild type strain to
look for global changes in mRNA profiles
 Grouping genes of similar expression profiles
 Using pathway analysis to putatively link the ORFan to a
Gene Ontology (GO) function.
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LEARNING GOALS
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Be able to access and use the basic search tools at
yeastgenome.org
Understand the process of RNAseq analysis from RNA
isolation through cDNA construction and sequencing.
Be able to load RNAseq data into the Galaxy platform for
quality assessment, transcriptome alignment and
differential expression analysis.
Be able to analyze differentially expressed genes for
putative pathway placement.
http://craftbeeracademy.com/wp-content/uploads/2012/09/yeast_large_winter.gif
VISION AND CHANGE CORE COMPETENCIES
1. ABILITY TO APPLY THE PROCESS OF SCIENCE:
2. ABILITY TO USE QUANTITATIVE REASONING :
3. ABILITY TO USE MODELING AND SIMULATION:
4. ABILITY TO TAP IN TO THE INTERDISCIPLINA RY NATURE OF
SCIENCE:
www.exploreyeast.com
VISION AND CHANGE CORE COMPETENCIES
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1. Ability to apply the process of science
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2. Ability to use quantitative reasoning
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Specifically, the understanding and using statistics to
analyze data
3. Ability to use modeling and simulation
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Specifically, the ability to interpret and analyze data
Specifically, the use of pathway analysis to assign gene
function
4. Ability to tap into the interdisciplinary nature of
science
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Specifically, learning and using computational
tools.
www.exploreyeast.com
TECHNOLOGY REQUIREMENTS
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GCAT-SEEK sequencing requirements
Use of Illumina HiSeq
 10-100 x 106 reads per sample, 50 – 150 nt
 Do not need long sequencing runs for RNAseq
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Program requirements for data analysis
Standard Mac or PC with internet access
 Galaxy account (is this enough computing power for a
yeast reference genome?)
 Do not need to assemble because Saccharomyces
reference genome is available
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www.mayo.edu
MODULE RESEARCH GOALS
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Goals of yeast ORFan project:
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organize a consortium of undergraduate researchers and PIs to assign
functions to S. cerevisiae ORFans.
pilot project for summer of 2013
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generate updated yeast ORFan list; draft a flow chart outlining process for
determining the function of yeast ORFans
begin to work through the drafted process with three selected ORFans
design and begin RNAseq analysis of expression profiles in two ORFan
deletion strains.
Full project: Students between consortium schools collaborate as teams
to assign a gene ontology (GO) term to a given ORFan.
Ultimately, the yeast orphan gene project aims to use the process of
determining ORFan gene function as a tool
to gain experience in scientific research,
collaboration and leadership.
www.bsse.ethz.ch