Fig. 2
Candidate selection from the SILAC-based quantitative proteomic analysis. (a) Volcano-plots of -log10 (p-value) as a function of the SILAC ratio per replicate. The vertical lines represent the first threshold used for biological variation (± 10%). The horizontal lines represent the threshold used for statistical significance (p-value ≤ 0.05). (b) Venn diagram of the number of proteins identified in each replicate as varying (absolute variation ≥10%, and p-value ≤ 0.05). (c) Histograms of the simulated distribution of shared proteins between replicates as estimated by the in-silico permutation test. Orange dashed vertical lines show ± 2 standard deviations from the mean. The blue vertical line in each graph shows the observed number of shared proteins in our experimental dataset for the corresponding comparison. (d) Criteria for candidate selection. (e) Functional classification of candidates using UniProtKB. Selected candidates are highlighted in blue.
