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Matt Settles Bioinformatics Core Washington State University Wednesday, April 23, 2008 WSU Linux User Group (LUG) . Bioinformatics at WSU. Biology. Computer Science. Statistics. What is Bioinformatics. The analysis of biological information using computers and statistical techniques. - PowerPoint PPT Presentation
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Bioinformatics at WSU
Matt SettlesBioinformatics Core
Washington State University
Wednesday, April 23, 2008WSU Linux User Group (LUG)
What is Bioinformatics
Computational Biologist
BioinformaticianBiostatistician
Biology
Computer Science
Statistics
The analysis of biological information using computers and statistical techniques
Subfields of Bioinformatics
Sequence analysis Main areas: Sequence alignment and Sequence
databases Genome annotation
Main areas: Gene finding, Gene predicting Computational evolutionary biology
Main areas: Systematics, Phylogenetics Analysis of High-throughput data
Main areas: RNA microarrays, aCGH, Whole genome genotyping arrays.
Analysis of Whole Genome Sequencing Data Emerging Field
Subfields of Bioinformatics
Comparative genomics How are species different and how are they the
same? Systems Biology
Networks of Networks (the golden goose!!) Quantitative Genetics Measuring Biodiversity Modeling biological systems High-throughput image analysis Analysis of protein expression Prediction of protein structure Protein-protein docking
What does a Bioinformatician Do?
Works in an interdisciplinary team Design of experiments Data management, databases Analysis from start to finish Data integration, annotation, visualization
Software Development Visual tools Databases
Research New techniques for the storage and analysis of
biological data, both statistical and compuational
What tools do we use
Software programs developed by others, GUI and command line Open Source preferably
Statistical Programming Languages/Environments R – programming environment
www.r-project.org www.bioconductor.org C like Interpreted language that acts similar to scheme, Full graphics capabilities C/python/perl interfaces
Software programs we ourselves develop
Central dogma of molecular biology
Each gene is transcribed (at the appropriate time) from DNA into mRNA, which then leaves the nucleus and is translated into the required protein.
Whole Genome Association Analysis
Whole Genome Genotyping Array Bovine (COW) 58,000 SNPs Illumina Beadarray Represents all 29 chromosomes, X chromosome
and the Unknown chromosome Samples
255 dairy cattle from 4 different heards 130 Control cattle (healthy) 125 Johne's positive cattle (sick)
14.8 MILLION DATA POINTS !!! Biological Question of interest
Is there a collection of SNPs that are associated with the disease Johne's?
Analysis Outline
Read in and format data into something we can work with in R and plink.
Quality Assurance Toss samples that do not meet QA (7 samples) Toss SNPs that do not meet QA (8,935 SNPs)
Treat SNPs as independent and analyze each with a statistical model.
Correct for multiple testing Visualize results
Results
10 regions were identified as being potentially interesting with a p < 0.001 multiple testing correction (permutation based)
Next Step
Validate in the lab, the regions of interest. Perform multi-locus analysis, computer
cluster will be necessary here. Mine the data for additional information
Job Position
Position with the Bioinformatics Core ~ 20 hours per week ~ $12-$15/hour Potential internship credit Description: Aid in the analysis of microarray
data, create analysis pipeline to be used by WSU researchers.
Required Skills: know how to code Bonuses: Possibility of publications!
The END
QUESTIONS??