Of all EFMs, which indicates a major role for network functionality. To gain a general overview of the higher biological processes of this set of reactions, we perform GO term over-representation analysis on their annotated genes (Additional file 1: Table S3). The clusters show significant enrichment for many processes crucial for cell growth, including amino acids (e.g., homoserine, serine, methionine, and lysine) biosynthesis, nucleotide, nucleoside and nucleobase interconversions, amine biosynthesis, coenzyme and carboxylic acid?Topfer et al. BMC Systems Biology 2012, 6:148 http://www.biomedcentral.com/1752-0509/6/Page 7 ofA0.3 0.2 0.1 0.B1 20.3 0.2 0.1 0.EFM fraction0.3 0.2 0.1 0.0 0.4 0.3 0.2 0.1 0.0EFM fraction0.3 0.2 0.1 0.0 0.4 0.3 0.2 0.1 0.Time in minTime in minA Cold: Fluctuating patterns: 2: Glycine Cleavage System, 3: L-threonine dehydrogenase, threonine synthase, aspartate-semialdehyde dehydrogenase, transaldolase, 4: phosphoglycerate mutase, Flat patterns: 7: acetylornithine transaminase, aspartate kinase, L-serine transport, aconitase, acetylornithine transaminase, adenylsuccinate lyase, aspartate kinase, purine-nucleoside phosphorylase (guanosine), pyrimidine-nucleoside phosphorylase (uracil), thymidine phosphorylase, thymidine kinase (ATP:thymidine), UDP-N-acetylglucosamine 2-epimerase, UTP-glucose-1-phosphate uridylyltransferase, UDPglucosehexose-1-phosphate uridylyltransferase, trimethylamine N-oxide reductase, glutathione reductase, 9: trehalose transport via PEP:Pyr (PTS), enolase, L-serine transport B Heat: Fluctuating patterns: 2: Glycine Cleavage System, 3: L-threonine dehydrogenase, threonine synthase, transaldolase, 5: Ammonia exchange, Flat patterns: 7: thymidine phosphorylase, aspartate kinase, 9: aconitase, adenylsuccinate lyase, trehalose transport via PEP:Pyr (PTS), enolase, acetylornithine transaminase, L-serine transport, purine-nucleoside phosphorylase (guanosine), pyrimidine-nucleoside phosphorylase (uracil), thymidine kinase (ATP:thymidine), UDP-N-acetylglucosamine 2-epimerase, UTP-glucose-1-phosphate uridylyltransferase, UDPglucose-hexose-1-phosphate uridylyltransferase, trimethylamine N-oxide reductase, glutathione reductaseFigure 3 Clustering of time-resolved fractional appearance profiles. Shown are the fractional appearance profiles of reactions over time. Under both (A) cold and (B) heat shock, the selected reactions group into 9 clusters. Enzyme names discussed in the text are given. A Nelfinavir (Mesylate) complete list of all enzyme names is given in the Additional file 1: Table S3. In both stresses clusters 7 and 9 represent metabolic reactions that are constantly PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/16989806 active, most of them crucial for viability. All other clusters represent reactions that undergo (de)activation and are likely involved in stress response. Note: For better visualization, identical profiles are slightly shifted. Reference value is given by the profile appearing on the bottom.metabolic processes as well as tricarboxylic acid (TCA) cycle. The reactions can further be grouped according to specific pathways. Closer inspection reveals a group of 3 constantly used reactions - aconitase, trehalose transport via PEP:Pyr (PTS) and enolase, which belong to the central carbon metabolism. The constant utilization of glucose uptake system (PTS) is not surprising, since it is crucial for culture grown on this nutrient, as well as for the formation of G6P and flux from PEP to pyruvate. Furthermore, this reaction has also been shown to be constitutive.