Systems Biology: The Next Frontier for Bioinformatics

Figure 2

A conceptualization of biochemical networks showing genome, transcriptome, proteome, and metabolome-level networks, highlighting their complexity and mutual interdependence. In biological systems a large number of structurally and functionally diverse components (genes, proteins, metabolites) are involved in dynamic, non-linear interactions, which in turn involve a range of time scales and interaction strengths. Direct conversions of species shown in solid lines, while some possible interactions (not necessarily one-step) are designated in dashed lines. Several types of interactions are shown: (1) enzyme catalysis, (2) posttranscriptional control of gene expression by proteins/protein complexes, including mechanisms that act on mRNAs (deadenylation, storage granulation) and mechanisms that act either directly or indirectly on DNA (histone modification, methylation), (3) effect of metabolite on gene transcription mediated by a protein, (4) protein-protein interaction, (5) effect of a downstream (“reporter”) metabolite on transcription through binding to a protein, (6) feedback inhibition/activation of an enzyme by a downstream metabolite, and (7) exchange of a metabolite with outside of the system (cell, organism).