1. What is the biological interpretation of the parameter b0 in the gene expression transcription factor binding site regression model as formulated here?

  • 2. Assume that you wanted to test all DNA patterns of length w = 6 for their association with gene expression. Explain how you could set up the FDR correction for this problem?
  • 3. How many parameters are estimated in the linear regression model with 216 transcription factors?
  • 4. It took 2 minutes for my laptop to fit (using R) all 216 multiple regression models I showed in the figures. Assuming each model takes about the same amount of time to fit, how long would it take to find the best possible model in this example?
  • 5. PBMs (protein binding microarrays) measure the binding affinity of DNA-binding proteins to every possible DNA sequence (up to length 10). Formulate the prediction of DNA-binding affinity as a multiple regression problem (what is Y ? what is X?).


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