1. Metabolic Networks Describe cellular reactions at the biochemical level –kinetics –thermodynamics –stoichiometry Several levels of hierarchy; the most useful: pathways and individual reactions Catabolism vs. anabolism; 11 common (central) metabolites Metabolite vs. enzyme graph Numerous genome-wide reconstruction efforts; most notable: E. coli and S. cerevisiae Amenable to analysis: individual and comparative

2. Signaling Transduction Networks Focus on control: transmission of extracellular signals into the nucleus Tend to have combinational properties (not as many cascades) Affect expression levels Reconstruction involves integration of multiple datatypes Not too many sources yet

3. Transcription Regulatory Networks Determine expression states (on/off) Activation vs. repression; degradation Study has focused on hierarchical decomposition (operons, regulons, stimulons) Mechanistics largely unknown; consequently: use of causal relationships and modules of all kinds Feedback, feed-forward and fan-out: dominant Easy to represent, quite a few resources

4. Protein-Protein Interaction Networks Both physical and genetic interactions Result of high throughput experiments Rather unreliable, but very popular…