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Figure 5 | BMC Bioinformatics

Figure 5

From: Dynamic covariation between gene expression and proteome characteristics

Figure 5

Gene expression in enriched Gene Ontology classes in the T cell dataset. The left array shows the gene ontology group receptor activity (4872), the middle array shows protein amino acid phosphorylation (6468), and the right array shows transcription factor activity (3700). Genes and proteins were annotated extensively. Signaling activities in the first two ontology classes are indicated by color coding of the block to the left of the expression patterns: protein tyrosine kinase (PTK, red), protein serine/threonine kinase (PSK, blue), dual-specificity kinase (DSK, cyan), receptor (R, black), and protein phosphatase (green). Genes are sorted based on their expression at time point 3. The box "" indicates the boundaries for significantly overexpressed, unchanged, and underexpressed genes at time point 3. Only 9% of receptor activity genes are significantly overexpressed, whereas 31% are significantly suppressed. All PSKs are located in the middle (i.e., changes in their gene expression at time point 3 are insignificant). Hypergeometric analysis revealed significant overrepresentation (p < 0.0008) of PSKs as well as significant underrepresentation of PTKs and Rs in this group. PTKs are overrepresented among the underexpressed genes (p < 0.005). When the genes are grouped according to the significance of their expression at time point 6, very significant over- and underrepresentation of PSKs is apparent among the groups of over- and underexpressed genes, respectively. A similar hypergeometric analysis for protein amino acid phosphorylation indicates consistently significant PSK underrepresentation and PTK overrepresentation among underexpressed genes at time point 3 and relative PSK enrichment and R depletion at time point 6. Significant depletion of membrane proteins and those integral to the plasma membrane appears at late time points (Figs. 2 and 3).

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