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MiDReG: Mining Developmentally Regulated Genes Debashis Sahoo PhD, Electrical Engineering, Stanford University Joint work with The Weissman Lab ICBP, Stanford University Integrative Cancer Biology Program, Stanford University Perspective 4878 Human Microarrays 2167 Mouse Microarrays Database of Dynamic ranges of each probesets RMA Poster #38 Jun Seita BooleanNet Database of Boolean implications Biology of HSC differentiation MiDReG Predicts developmentally regulated genes Debashis’ Poster MiDReG Identifies a branchpoint between B and T cell development Poster #17 Matt Inlay ICBP, Stanford University Motivation Hard to discover using other approaches Genetics Biochemistry These genes carry out important functions Development and differentiation Surface markers are easy to study ICBP, Stanford University BooleanNet Get data GEO [Edgar et al. 02] Normalize RMA [Irizarry et al. 03] Determine thresholds Discover Boolean relationships Biological interpretation Sahoo et al. Genome Biology 2008 ICBP, Stanford University Determine threshold High Intermediate Low Threshold Sorted arrays A threshold is determined for each gene. The arrays are sorted by gene expression StepMiner is used to determine the threshold [Sahoo et al. 07] ICBP, Stanford University Discovering Boolean Implications 4 1 3 GABRB1 2 Analyze pairs of genes. Analyze the four different quadrants. Identify sparse quadrants. Record the Boolean relationships. ACPP high GABRB1 low GABRB1 high ACPP low ACPP Sahoo et al. Genome Biology 2008 ICBP, Stanford University Six Boolean Implications Sahoo et al. Genome Biology 2008 ICBP, Stanford University B X A A Prediction of Developmentally Regulated Genes X ICBP, Stanford University B Computational Discovery of Human B Cell Precursors ICBP, Stanford University qPCR Results Test: Median1 < Median2 10/14 pass (FDR 14%) × × ICBP, Stanford University × × More B Cell Precursors ICBP, Stanford University Validation ICBP, Stanford University 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. ICBP, Stanford University 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 wellcharacterized developmental pathway ICBP, Stanford University Acknowledgements David L. Dill Sylvia K. Plevritis Robert Tibshirani Irving L. Weissman The Weissman Lab: Deepta, Jun, Matt Funding: ICBP Program (NIH grant: 5U56CA112973-02) ICBP, Stanford University The END ICBP, Stanford University Statistical Tests Compute the expected number of points under the independence model nAlow = (a00+ a01), nBlow = (a00+ a10) total = a00+ a01+ a10+ a11, observed = a00 expected = (nAlow/ total * nBlow/ total) * total B a01 a11 a00 a10 A Compute maximum likelihood estimate of the error rate error rate = 1 2 ( (a a00 00+ a01) + a00 (a00+ a10) ) ICBP, Stanford University