Consequently, the interesting cases are those that deviate from the trivial pattern, either by a stronger than normal down-regulation, by an up-regulation, or by a specific effect of TGFβ. Would it have been possible to obtain the same results with alternative approaches that relate transcript data to metabolic functions? Often, metabolic functions are represented by metabolic subsystems defined for instance by GO terms [35] or KEGG Inhibitors,research,lifescience,medical maps [36], e.g., tyrosine degradation is represented in the KEGG map 00350. But this map also includes synthesis of thyridoxine,
tyramine, hydroxyphenylacetate, dopaquinone, eumelanine, adrenaline, metanephrine, 3-methoxy-4-hydroxymandelate, 3-methoxy-4-hydroxy-phenylethylene-glycol, and SCR7 molecular weight homovanillate (only genes present in mice are considered). Most of these synthesis pathways are specific to other cell types and are switched off in hepatocytes. Thus, tyrosine degradation is represented by only 5 out of 37 genes related to this KEGG map. So the down-regulation Inhibitors,research,lifescience,medical of genes
involved in tyrosine degradation Inhibitors,research,lifescience,medical would not be particularly remarkable considering the fact that many metabolic genes are down-regulated (see Section 2.1). The system of KEGG modules [37] represents small functional pathways. The module M00044 for example would indeed represent the 5 genes for tyrosine degradation. However, the set of KEGG modules is a fixed and restricted set of pathways and does not cover comprehensively all relevant metabolic functions, Inhibitors,research,lifescience,medical considering that the 260 modules cover pathways in cells in all kingdoms of life. For instance, hepatic ethanol degradation is not such a module. Both classification schemes would ignore any transporters (which is for instance very relevant for glucose release), supply of initial substrates, and disposal of side products (see for instance the urea synthesis, several reactions are apparently coupled to the urea cycle although belonging to amino acid metabolism in the first place). Gene ontology annotations are available from various sources. For instance, the gene Inhibitors,research,lifescience,medical ontology term tyrosine catabolic process GO:0006572 would have recovered the
five genes using the annotation of the Brainarray chip definition file. For this pathway, the much GO term tyrosine catabolic process to fumarate (GO:0019445) would even be more appropriate, but this annotation is not present in the data annotation deposited at Ensemble/BioMART. For several appropriate GO terms of ethanol detoxification, no genes are annotated to the enzymes involved (alcohol dehydrogenase and aldehyde dehydrogenase) as they are multi-specific. The GO annotation provides only a set of genes connected to the function, whereas a specific role is not asserted but would be given by the flux distribution annotated with genes. Often, to assess the regulation of such a subsystem, the number of gene changes above a certain threshold (usually 2-fold) is counted.