THE YEAST ORPHAN GENE PROJECT: FINDING A PLACE FOR ORFANS TO “GO”

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

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

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

1. Ability to apply the process of science Specifically, the ability to interpret and analyze data

2. Ability to use quantitative reasoning Specifically, the understanding and using statistics

to analyze data 3. Ability to use modeling and simulation

Specifically, the use of pathway analysis to assign gene function

4. Ability to tap into the interdisciplinary nature of

science Specifically, learning and using computational tools.

www.exploreyeast.com

VISION AND CHANGE CORE COMPETENCIES

TECHNOLOGY REQUIREMENTS

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

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

www.mayo.edu

MODULE RESEARCH GOALS

Goals of yeast ORFan project: organize a consortium of undergraduate researchers and PIs

to assign functions to S. cerevisiae ORFans. pilot project for summer of 2013

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