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

4. Modeling

5. 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?

6. 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

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

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