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Relating Factors and Gene Lists

Relating Factors and Gene Lists. Biological Pathway. Microarray Experiment Genes differentially expressed Signature, in vitro. Protein Interactions Genes predicted based on promoters?. ?. BFRM Factors, in vivo Decomposition of signature Probability for each gene and each factor.

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Relating Factors and Gene Lists

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  1. Relating Factors and Gene Lists

  2. Biological Pathway • Microarray Experiment • Genes differentially expressed • Signature, in vitro • Protein Interactions • Genes predicted based on promoters? ? • BFRM • Factors, in vivo • Decomposition of signature • Probability for each gene and each factor

  3. Modeling

  4. Results • Useful for comparing factors to a fixed rule • Model for imputing {pi}from {wi}? • Uniform priors on ui and wi? • Adapt for assessing similarity between factors?

  5. E2F3 • Y is TFE3, Z is SMAD3 • Specific to E2F3 • 108 genes - 264 probes A Z E2F Y 1027 times more likely • Factor 2 contains ¼ 650 probes at > 99% • 50 probes in the intersection

  6. Factor 2 vs Rule 3b >99% Factor 3 Above black line Rule 3b genes tfe3 – smad3 Factor 2 > 99% not in database Samples (Miller)

  7. Known to down-regulate SMAD-3 • Found from factor analysis • Not in the rule 3B data set

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