1. MiDReG: Mining Developmentally Regulated Genes
Debashis Sahoo
PhD, Electrical Engineering, Stanford University
Joint work with The Weissman Lab
Integrative Cancer Biology Program, Stanford University
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Perspective
RMA
Database of
Dynamic ranges of each probesets
4878 Human Microarrays
2167 Mouse Microarrays
Poster #38
Jun Seita
BooleanNet
MiDReG
Database of
Boolean implications
Predicts developmentally regulated genes
Debashis’ Poster
MiDReG
Identifies a branchpoint between B and T cell development
Poster #17
Matt Inlay
Biology of
HSC differentiation
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Motivation
Hard to discover using other approaches
Genetics
Biochemistry
These genes carry out important functions
Development and differentiation
Surface markers are easy to study
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BooleanNet
Get data
GEO
[Edgar et al. 02]
Normalize
RMA
[Irizarry et al. 03]
Determine thresholds
Discover Boolean relationships
This is an overview of the Boolean analysis.
- brain image
Make it more professional.
Flow chart
Biological interpretation
Sahoo et al. Genome Biology 2008
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Determine threshold
A threshold is determined for each gene.
The arrays are sorted by gene expression
StepMiner is used to determine the threshold
High
CDH expression
Intermediate
Threshold
Low
Say about linear shape.
Labels in the graph bigger.
Put forbidden zone
threshold. Labels.
Sorted arrays
[Sahoo et al. 07]
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6. Discovering Boolean Implications
Analyze pairs of genes.
Analyze the four different quadrants.
Identify sparse quadrants.
Record the Boolean relationships.
ACPP high  GABRB1 low
GABRB1 high  ACPP low 2 4
GABRB1 1 3
If -> then
Describe x and y axis.
Describe a point.
Statistical tests for identifying sparse quadrant.
ACPP
Sahoo et al. Genome Biology 2008
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7. Six Boolean Implications
Sahoo et al. Genome Biology 2008
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8. Prediction of Developmentally Regulated GenesB A X
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9. Computational Discovery of Human B Cell Precursors
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qPCR Results
Test: Median1 < Median2
10/14 pass (FDR 14%) × × × ×
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More B Cell Precursors
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Validation
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13. Analysis of Predicted Genes
Total number of genes predicted: 62
33 genes have been knocked out in mice. [Literature]
18 genes have defects in B cell function and B cell differentiation.
2 genes are known prognostic markers of B cell lymphomas: WASPIP and GCET2.
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Conclusion
MiDReG uses Boolean implications to predict genes related to B cell development
Knockouts of the predicted genes have defects in B cell function and differentiation
MiDReG can be directly applied to other less well-characterized developmental pathway
Write this carefully to summarize the key points.
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Acknowledgements
David L. Dill
Sylvia K. Plevritis
Irving L. Weissman
The Weissman Lab:
Deepta, Jun, Matt
Robert Tibshirani
Same font size.
Funding: ICBP Program (NIH grant: 5U56CA )
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The END
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Statistical Tests
Compute the expected number of points under the independence model
Compute maximum likelihood estimate of the error rate
a00
a01
a11
a10 A B
nAlow = (a00+ a01), nBlow = (a00+ a10)
total = a00+ a01+ a10+ a11, observed = a00
expected = (nAlow/ total * nBlow/ total) * total
a00
(a00+ a01)
(a00+ a10) + ( ) 1 2
error rate =
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