Figure 2

Correlation analysis of the dataset for stimulated T cells. Visualization of Spearman's linear correlations between gene expression and protein properties in T cells stimulated with CD3 (left) or costimulated with CD3/CD28 (right). The columns represent time points 1 to 6 corresponding to 1, 2, 6, 12, 24 and 48 hr after stimulation. The 114 variables (rows) consist of 20 amino acid proportions described by three-letter abbreviations, 29 sequence- or amino acid composition-derived parameters (panels to the left), 50 gene ontologies (marked by GO at the beginning), four predicted subcellular localizations (specified by SubLoc), and 11 structural parameters from SCOP (panels to the right). Correlation coefficients are color-coded. Red indicates a positive correlation; i.e., increased production of proteins, which is either attributed to a property (within the categories of GO, SCOP, or SubLoc) or to higher proportions of a property (including amino acids and physicochemical parameters), leading to relative enrichment of that property. Green indicates a negative correlation; i.e., reduced production of proteins, which is either attributed to the property or to higher proportions of the property, leading to relative depletion of that property. The magnitude of the correlation coefficients is represented by color intensity, as indicated at the bottom. The range is from -0.12 to 0.12 for sequence-derived parameters and -0.7 to 0.7 for categorical data used in the TOC approach. The numbers in brackets indicate the genes for which gene ontologies, subcellular localization or structural classes were identified. The correlation coefficients are clustered using the SOM method so as to group features manifesting similar patterns.