Figure 4

Two-dimensional hierarchical clustering of refined experimental phenotypes. Experimental phenotypic profiles for those strains that showed reduced growth under at least one condition were clustered using two-dimensional hierarchical clustering. The rows are different genes and the columns are the 16 experimental conditions present in the current data set. Each entry is representative of the phenotype of the knockout of a particular gene under a particular condition, with more severe phenotypes being represented with darker shades of gray. Prominent clusters have been boxed, and the most significantly enriched Gene Ontology biological process terms among the genes in each cluster are noted to the right. This representation allowed for several immediate observations. For example, it can be seen that the red and purple clusters primarily contain mutants that show a phenotype only under non-fermentable carbon sources. Fitting expectations, process analysis revealed that the majority of the genes in these clusters participate in respiratory function. Another observation that fits with biological intuition is the enrichment of amino acid biosynthetic genes in the green cluster, which encompasses only the minimal media condition. Given that the other conditions lack, at most, only an individual amino acid, it fits with expectations that most amino acid biosynthetic genes should be essential only in the condition where all amino acids, except those for which the utilized strain cannot produce (for example, histidine and leucine), are absent. The remaining clusters capture more diverse sets of genes, and individual Gene Ontology terms are not as illuminating as to the metabolic challenges faced under the conditions encompassed by the given clusters.