Visualization of the two most significant "up-regulated neighborhoods" identified by GiGA using a metabolic network derived from Swissprot annotations. The expression data are taken from the 20.5 h timepoint of the yeast diauxic shift (DeRisi et al., 1997). The layout was generated as in Fig 2. Colored boxes show the regulated genes (darker shading indicates stronger regulation), white boxes show the substrates that are in common between genes. Important components of this regulatory neighborhood are indicated (TCA cycle and glyoxylate cycle enzymes, and the various respiratory chain complexes). Here it can be seen that GiGA not only detects protein complexes (such as ribosomes or the respiratory chain complexes), but also "linear" metabolic pathways such as TCA cycle and glyoxylate cycle (and potentially signal transduction pathways or regulatory cascades etc.). Almost all the enzymes discussed by DeRisi et al. (1997) are included in these two subgraphs, plus the relevant enzymatic information necessary to assess the relevance of each link, without the danger of missing some genes (unless the annotation is incomplete).
Breitling et al. BMC Bioinformatics 2004 5:100 doi:10.1186/1471-2105-5-100