the yeast orphan gene project finding a place for orfans to go n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
The Yeast Orphan Gene Project: Finding a place for ORFans to “GO” PowerPoint Presentation
Download Presentation
The Yeast Orphan Gene Project: Finding a place for ORFans to “GO”

Loading in 2 Seconds...

play fullscreen
1 / 7

The Yeast Orphan Gene Project: Finding a place for ORFans to “GO” - PowerPoint PPT Presentation


  • 95 Views
  • Uploaded on

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.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'The Yeast Orphan Gene Project: Finding a place for ORFans to “GO”' - muniya


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
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.

The Yeast Orphan Gene Project: Finding a place for ORFans to “GO”
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.
Module Research Goals

https://encrypted-tbn2.gstatic.com/images?q=tbn:ANd9GcQpx-HhripNInzlpjfIepFTmma0q8k-okvJq9_9Uml0SjsssDgPag

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

Learning goals
vision and change core competencies
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 competencies1

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 IlluminaHiSeq
    • 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
Technology requirements

www.mayo.edu

module research goals1

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

Module Research Goals