Lucia I. Ramirez Week 13

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Create the Input Excel Workbook for the Model

  1. My file was similar to the file "Input_4_gene_forward_correct_params.xlsx" that I used in class on Tuesday, but with my expression data and network. I downloaded this file, changed the name to "Input_4_gene_forward_correct_params_Lsquared.xlsx" , and edited it to include my data. (The file can be found in this zipped file on LionShare.)
    • Copied the transposed matrix from my "network" sheet and paste it into the worksheets called "network" and "network_weights".
    • Kept transcription factors in the same order for all of the worksheets.
  2. The next worksheet to edit is the one called "degradation_rates".
    • Pasted my list of transcription factors from your "network" sheet into the column named "StandardName". Looked up the "SystematicName" of your genes. YEASTRACT has a feature that will allow you to paste your list of standard names in to retrieve the systematic names here.
    • Next, looked up the degradation rates for my list of transcription factors. These rates have been calculated from protein half-life data from a paper by Belle et al. (2006). Looked up the rates for transcription factors from this file and included them in "degradation_rates" worksheet. If a transcription factor did not appear in the file above, I used the value "0.027182242" for the degradation rate.
  3. The next worksheet to edit is the one called "production_rates".
    • Pasted the "SystematicName" and "StandardName" columns from my "degradation_rates" sheet into the "production_rates" sheet.
    • The initial guesses for the production rates using for the model are two times the degradation rate. Computed these values from degradation rates and pasted the values into the column titled "ProductionRate".
  4. Next inputed the expression data for the wild type strain and the other strain (dhmo1). I only included the data for the genes in my network, in the same order as they appear in the other worksheets.
    • Put the wild type data in the sheet called "wt".
    • The sample spreadsheet has a worksheet named "dcin5". Changed this name to dhmo1.
    • Pasted the SystematicName and StandardName columns from one of your previous sheets into this one.
    • The data in this sheet is the Log Fold Changes for each replicate and each timepoint from Week 11 Assignment. I only used the cold shock timepoints for the modeling. Thus your column headings for the data should be "15", "30", and "60". There will be multiple columns for each timepoint (typically 4) to represent the replicate data, but they will all have the same name.
    • Copy and pasted the data from your Week 11 spreadsheet into this one. You need to include only the data for the genes in your network. Make sure that the genes are in the same order as in the other sheets.
  5. Edited the following parts of the "optimization_parameters" worksheet.
    • For the parameter "time" (Cell A13), replaced what is in the sample file with "15", "30", and "60", since these are the timepoints we have in our data.
    • For the parameter "Strain" (Cell A14), replaced "dcin5" with dhmo1, making sure that the capitalization and spelling is the same as what you named the worksheet containing that strain's expression data.
    • For the parameter "Deletion", left the zero in cell B15. In cell C15, put a number corresponding to the position in the list of gene names that the gene that was deleted appears. In my file, HMO1 is number 13 in the list of 13 genes.
    • For the parameter "simtime", you perform the forward simulation of the expression in five minute increments from 0 to 60 minutes. Thus, this row should read: "simtime", "0", "5", "10", ..., "60".
  6. The last sheet modified called "network_b".
    • Pasted in the list of standard names for your transcription factors from one of your previous sheets. Note that this sheet does not have a column for the systematic name.
    • Cell A1 in the sample files has the text "rows genes affected/cols genes controlling".
    • The "threshold" value for each gene should be "0".

Final Result of Input Excel Workbook

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