Jonathan Nowacki School of Informatics Master of Science in Bioinformatics Sun Kim Ph'D' Mimi Zolan

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Jonathan NowackiSchool of Informatics Master of
Science in BioinformaticsSun Kim Ph.D. Mimi
Zolan Ph.D.
Discovery and Visualization of Germline Genes in
a Mushroom with Synchronous Cellular Division
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Outline

• Background Goals
• The Mushroom
• Microsatellites
• Exon Prediction
• Microarray
• Gbrowse
• Summary
• Acknowledgments

Outline
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Cellular Division

• Importance
• Aging
• Cancer
• Disease
• Stem cell research
• Reproduction

Outline
Background
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Goals

• Partial Genome
• Use Microsatellite data to find a region of
  importance
• Predict Exons using FGENE
• Whole Genome
• Use Microarray data to find a genes that are
  up-regulated in germ line cells.
• Visualization
• Gbrowse

Outline
Background
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Background on progress

• Whats been done
• Rad3/Rad9 Mre11
• MIT Whitehead Institute
• Southeast Missouri
• Problems
• Coprinus isnt mapped
• Converging data
• NBS1

Outline
Background
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Why Coprinus?
Outline
Background

• Its not a mammal
• Short life cycle
• Synchronous division
• Easy to maintain

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Partial Genome

• Wet lab
• Locate an area of interest
• Focus on NBS1
• DNA repair
• Expressed during meiosis
• Exon Prediction
• FGENE

Outline
Background
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Microsatellite Search

• Purpose
• Locate genes with known phenotype but unknown
  sequence.
• Locate area of interest.
• Tools
• GCG, Findpatterns
• 119 microsatellites were used

Outline
Background
Microsatellites
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What is a microsatellite?

• AAAAA
• CACACA
• CTTCTTCTT

Outline
Background
Microsatellites
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Utility of Microsatellites

• 8C11

Outline
Background
Microsatellites
Microsatellites
Microsatellites
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Recombination
Outline
Background
Microsatellites
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Finding Microsatellites
GCG Find patterns
Outline
Background
Microsatellites
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Electrophoresis
Outline
Background
Microsatellites
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Electrophoresis
Outline
Background
Microsatellites
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Finer resolution

• Micro satellites are small
• Agarose wasnt good enoug
• High grade Fufi agarose wasnt good enough
• Moved to polyacrylamide

Outline
Background
Microsatellites
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Finest resolution
Outline
Background
Microsatellites
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Mapping
Outline
Background
Microsatellites
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Microsatellite Results

• Microsatellites were found
• Polymorphism was low, for a variety of reasons,
  but a few usable markers were found
• Wasnt the most effective method

Outline
Background
Microsatellites
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Exon Prediction

• Used to find and predict genes
• FGENE
• Hidden Markov models
• Compared to known genes
• Exons blasted vs. NCBI NR

Outline
Background
Microsatellites
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FGENE highlights

• Phanerochaete chrysosporium
• 220 exons predicted
• Cryptococcus neoformans
• 216 exons predicted
• Ustilago
• 234 exons predicted

Outline
Background
Microsatellites
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Exons
Outline
Background
Microsatellites
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Blast

• 6 frame translation
• ATGCTCGGGACTGATCGA
• ATGCTCGGGACTGATCGA
• ATGCTCGGGACTGATCGA
• TCGATCAGTCCCGAGCAT

Outline
Background
Microsatellites
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Phase 2 Whole Genome

• Microarray
• Map genes active in meiosis
• Visualization
• Gbrowse

Outline
Background
Microsatellites
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Microarray
Outline
Background
Microsatellites
Microarray
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Microarray
Outline
Background
Microsatellites
Microarray
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Germ line
Outline
Background
Microsatellites
Microarray
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Results

• Drosophila
• 254 / 781
• 633 / 2340
• Worm
• 553 / 2496
• Testis Fly
• pending

Outline
Background
Microsatellites
Microarray
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Visualizing the Genome

• Data
• Microarray
• Microsatellite
• Exon
• Needs
• Easy analysis of genetic data
• Doesnt require computer science background
• Web based for portability.

Outline
Background
Microsatellites
Microarray
Gbrowse
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Gbrowse
Outline
Background
Microsatellites
Microarray
Gbrowse
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Default Values
Outline
Background
Microsatellites
Microarray
Gbrowse
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Solution A Dynamic database
Outline
Background
Microsatellites
Microarray
Gbrowse
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More Specificity
Outline
Background
Microsatellites
Microarray
Gbrowse
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Highly Specific
Outline
Background
Microsatellites
Microarray
Gbrowse
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Summary

• Coprinus is ideal for studying cellular division
• Microsatellite data for mapping
• Microarray data for gene function
• Gbrowse visualization
• Dynamic Database

Outline
Background
Microsatellites
Microarray
Gbrowse
Summary
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Conclusion

• Gbrowse
• Microarray comparisons
• Exon Prediction
• Microsatellites

Outline
Background
Microsatellites
Microarray
Gbrowse
Summary
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Acknowledgments

• Dr. Sun Kim
• Dr. Mimi Zolan
• Dr. Haixu Tang
• Dr. John Colbourne
• Henry Paik
• Danny Rice

Outline
Background
Microsatellites
Microarray
Gbrowse
Summary
Acknowledgments