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For each gene, we calculated protein expression level as a median copy number of all peptides mapped to any of the isoforms corresponding to this gene.
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The SILAC results can also be used to calculate protein expression-based repression.
To calculate a protein expression index, the percentage score was summed with the intensity score.
The data were analysed using the ProteinAssist Software 1.0 (Applied Biosystems), which uses the ΔCt method to calculate relative protein expression between untreated controls and treated samples.
Following this operation it has been possible to calculate average protein expression and to infer protein differential expression between breast cancer tissues and normal tissues as difference between two protein expression scores.
To calculate predicted protein expression, the estimated mRNA and miRNA coefficients from the Oslo2 cohort were fitted into equation (4) using the actual miRNA and mRNA expression data of the DBCG and TCGA data sets, respectively.
The Food and Drug Administration's basic formula for calculating protein needs is.8 grams of protein for every kilogram of body weight.
Differential expression ratios for proteins were obtained from Protein Pilot™ which calculates protein ratios using only ratios from the spectra that are distinct to each protein, excluding the shared peptides of protein isoforms.
Averages and standard deviations were calculated for each protein expression value when multiple peptide measurements were available.
The apparent Km, Vmax, and corrected Vmax values (calculated based on protein expression levels) have been summarized in Table 2.
The relative expression level was calculated: (indicated group protein expression level / loading control expression level) / (control group protein expression level / loading control expression level).
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