3. Analysis Output Table

The Python script (peca_[name].py) will produce the following output:

data_R_CPS.txt

This file contains log_e-transformed mRNA and protein data, rate parameters and change points scores. Columns headers are as follows. The symbol "x" in the header indicates a time point (e.g. R0 is the rate or rate ratio in the first time period):

• Rx
  • synthesis rates for PECA-R and PECA-pS
  • rates ratios for PECA and PECA-N
• signedCPSx: change point score (for PECA, PECA-N) or synthesis change point score(for PECA-R, PECA-pS) by the direction of change (’-’ indicates down regulation).
• PECA-core and PECA-N only
  • FDRx: false discovery rates for rate ratios
• PECA-R and PECA-pS only
  • Dx: degradation rates
  • signedCPDx: change point score for degradation rates by the direction of change (’-’ indicates down regulation).
  • FDR_Sx: FDR for changes in synthesis rates
  • FDR_Dx: FDR for changes in degradation rates

mRNAprot.pdf

Gene-specific plots.

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GSA module gives the following output:

Goterms.txt

A table of p-values corresponding to the CPS in PECA analysis. Columns headers are:

• GO_size: number of genes in the pathway
• GO_EdgeCount (PECA-N only): number of edges connecting the gene.
• GO_size_background: number of genes in the pathway that appears in the experimental data.
• Upx: p-value for enrichment based on the number of up-regulated genes
• MaxSig(Up): maximum of −log₁₀(Upx) of all time points.
• Downx: p-value for enrichment based on the number of down-regulated genes
• MaxSig(Down): maximum of −log₁₀(Downx) of all time points.
• Sigx: p-value for enrichment based on the number of up-regulated and down-regulated genes
• Max(Both): maximum of −log₁₀(Sigx) of all time points.