Download Outline - Bioinformatics at School of Informatics, Indiana University

Discovery and Visualization of
Germline Genes in a Mushroom with
Synchronous Cellular Division
Jonathan Nowacki
School of Informatics
Master of Science in Bioinformatics
Sun Kim Ph.D.
Mimi Zolan Ph.D.
Zolan Lab
Outline
Outline
Zolan Lab
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Background & Goals
The Mushroom
Microsatellites
Exon Prediction
Microarray
Gbrowse
Summary
Acknowledgments
Cellular Division
Importance
Outline
Background
Zolan Lab
– Aging
– Cancer
– Disease
– Stem cell research
– Reproduction
Goals
1. Partial Genome
Outline
Background
– Use Microsatellite data to find a
region of importance
– Predict Exons using FGENE=
2. Whole Genome
– Use Microarray data to find a genes
that are up-regulated in germ line
cells.
3. Visualization
– Gbrowse
Zolan Lab
Background on progress
Outline
Background
What’s been done
• Rad3/Rad9 Mre11
• MIT Whitehead Institute
• Southeast Missouri
Problems
• Coprinus isn’t mapped
• Converging data
• NBS1
Zolan Lab
Why Coprinus?
Outline
Background
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Zolan Lab
It’s not a mammal
Short life cycle
Synchronous division
Easy to maintain
Partial Genome
1. Wet lab
Outline
Background
– Locate an area of interest
– Focus on NBS1
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DNA repair
Expressed during meiosis
2. Exon Prediction
– FGENE
Zolan Lab
Microsatellite Search
• Purpose
Outline
Background
Microsatellites
– Locate genes with known
phenotype but unknown
sequence.
– Locate area of interest.
• Tools
– GCG, Findpatterns
– 119 microsatellites were used
Zolan Lab
What is a microsatellite?
Outline
Background
Microsatellites
Zolan Lab
AAAAA
CACACA
CTTCTTCTT
Utility of Microsatellites
8C11
Outline
Background
Microsatellites
Microsatellites
Microsatellites
Zolan Lab
Recombination
Outline
Background
Microsatellites
Zolan Lab
Finding Microsatellites
GCG – Find patterns
Outline
Background
Microsatellites
Zolan Lab
Electrophoresis
Outline
Background
Microsatellites
Zolan Lab
Electrophoresis
Outline
Background
Microsatellites
Zolan Lab
Finer resolution
• Micro satellites are small
Outline
Background
Microsatellites
Zolan Lab
– Agarose wasn’t good enoug
– High grade “Fufi” agarose wasn’t
good enough
– Moved to polyacrylamide
Finest resolution
Outline
Background
Microsatellites
Zolan Lab
Mapping
Outline
Background
Microsatellites
Zolan Lab
Microsatellite Results
Outline
Background
Microsatellites
Zolan Lab
• Microsatellites were found
• Polymorphism was low, for a
variety of reasons, but a few
usable markers were found
• Wasn’t the most effective
method
Exon Prediction
• Used to find and predict genes
Outline
Background
Microsatellites
– FGENE
– Hidden Markov models
• Compared to known genes
– Exons blasted vs. NCBI NR
Zolan Lab
FGENE highlights
• Phanerochaete chrysosporium
Outline
Background
Microsatellites
– 220 exons predicted
• Cryptococcus neoformans
– 216 exons predicted
• Ustilago
– 234 exons predicted
Zolan Lab
Exons
Outline
Background
Microsatellites
Zolan Lab
Blast
Outline
Background
Microsatellites
• 6 frame translation
ATGCTCGGGACTGATCGA
ATGCTCGGGACTGATCGA
ATGCTCGGGACTGATCGA
TCGATCAGTCCCGAGCAT
Zolan Lab
Phase 2: Whole Genome
• Microarray
Outline
Background
Microsatellites
Zolan Lab
– Map genes active in meiosis
• Visualization
– Gbrowse
Microarray
Outline
Background
Microsatellites
Microarray
Zolan Lab
Microarray
Outline
Background
Microsatellites
Microarray
Zolan Lab
Germ line
Outline
Background
Microsatellites
Microarray
Zolan Lab
Results
• Drosophila
Outline
Background
Microsatellites
Microarray
– 254 / 781
– 633 / 2340
• Worm
– 553 / 2496
• Testis Fly
– pending
Zolan Lab
Visualizing the Genome
• Data
Outline
Background
Microsatellites
Microarray
Gbrowse
– Microarray
– Microsatellite
– Exon
• Needs
– Easy analysis of genetic data
– Doesn’t require computer
science background
– Web based for portability.
Zolan Lab
Gbrowse
Outline
Background
Microsatellites
Microarray
Gbrowse
Zolan Lab
Default Values
Outline
Background
Microsatellites
Microarray
Gbrowse
Zolan Lab
Solution: A Dynamic
database
Outline
Background
Microsatellites
Microarray
Gbrowse
Zolan Lab
More Specificity
Outline
Background
Microsatellites
Microarray
Gbrowse
Zolan Lab
Highly Specific
Outline
Background
Microsatellites
Microarray
Gbrowse
Zolan Lab
Summary
Outline
Background
Microsatellites
Microarray
Gbrowse
Summary
Zolan Lab
• Coprinus is ideal for studying
cellular division
• Microsatellite data for mapping
• Microarray data for gene
function
• Gbrowse visualization
• Dynamic Database
Conclusion
Outline
Background
Microsatellites
Microarray
Gbrowse
Summary
Zolan Lab
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Gbrowse
Microarray comparisons
Exon Prediction
Microsatellites
Acknowledgments
Outline
Background
Microsatellites
Microarray
Gbrowse
Summary
Acknowledgments
Zolan Lab
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Dr. Sun Kim
Dr. Mimi Zolan
Dr. Haixu Tang
Dr. John Colbourne
Henry Paik
Danny Rice