Relating Factors and Gene Lists

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Relating Factors and Gene Lists
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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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Modeling
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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?

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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 gt 99
• 50 probes in the intersection

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Factor 2 vs Rule 3b
gt99 Factor 3 Above black line
Rule 3b genes tfe3 smad3
Factor 2 gt 99 not in database
Samples (Miller)
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• Known to down-regulate SMAD-3
• Found from factor analysis
• Not in the rule 3B data set