1. Preparing Input Parameter File

PECA expects three mandatory input files. These include gene data, protein data. The last file is a container for input parameters, which describes the name of the two data files, the number of replicates, and the time points (example files can be found in the examples folder).

The PECA software requires that the user provide the following parameters for data processing and modeling:

• FILE_X:
  Name of the tab-delimited file containing the mRNA data.
  Append 0 after a whitespace to switch off log_e-transformation (e.g., FILE_X = mRNA_data.txt 0).
• FILE_M (PECA-pS only):
  Name of the tab-delimited file containing the M channel (degradation proxy) data.
  Append 0 after a whitespace to switch off log_e-transformation.
  The PECA software will match rows between mRNA and protein data by gene IDs, and only gene IDs that appear in all 3 files FILE_M, FILE_X and FILE_Y will be analyzed.
• FILE_Y:
  • for PECA-pS: Name of the tab-delimited file containing the H channel (synthesis proxy) data.
    Append 0 after a whitespace to switch off log_e-transformation.
    The PECA software will match rows by gene IDs, only gene IDs that appear in all 3 files FILE_M, FILE_X and FILE_Y will be analyzed.
  • for all other PECA modules: Name of the tab-delimited file containing the protein data.
    Append 0 after a whitespace to switch off log_e-transformation.
    The PECA software will match rows by gene IDs, only gene ID that appear in both FILE_X and FILE_Y will be analysed.
• TIME: The time points.
• SMOOTHING: The smoothing parameters. The first number sets the value of F. The second number sets the value of l (see supplementary information). Remove line if no smoothing is required.
• N_BURN: Number of burn-in in the MCMC sampler.
• N_THIN: Number of thinning in the MCMC sampler.
• N_SAMPLE: Number of MCMC samples to collect.
  Note that
  (total number of iterations) = N_BURN + N_THIN × N_SAMPLE

If module data (network information) is used, the following options need to be set:

• MODULE: Name of the file containing the module data. Exclude this line when module data is not used.

Next, PECA GSA software requires that the user provide the following options for data processing and modeling:

• FDR_cutoff: FDR cutoff for the selection of genes. Values should be between 0 and 1.
• GO_term_table: Pathway / gene group / biological function data. Gene IDs should be consistent between this file and the input data.
• BACKGROUND: The first number is the minimum percentage of genes in ’data R CPS’ for a pathway to be analysed. This value should be between 0 and 100. The second number is the minimum number of genes that must be selected for an particular pathway to tested (otherwise p-value of 1 is reported for the pathway). This value should be a positive integer.
• SYNTHESIS (PECA-R, PECA-pS only): 1 to indicate GSA on the synthesis rates, 0 to indicate GSA on the degradation rates.