ADAGE extracted features that represented sequence differences between strains. ADAGE extracted features that represented sequence differences between.

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ADAGE extracted features that represented sequence differences between strains. ADAGE extracted features that represented sequence differences between strains. (A) ADAGE node activity heat map analysis of the genome hybridization of P. aeruginosa strains PA14 and PAO1 to Affymetrix Pseudomonas GeneChips. The heat map shows the ADAGE activity differences of each node in each strain when the genome hybridization data were analyzed. The activity values of node 30 most strongly differentiated strains PAO1 and PA14. (B) Analysis of mean centered node 30 activity values clearly distinguished strain PAO1 from other P. aeruginosa strains (HM4, E601) or uncharacterized CF strains in RNA expression experiments. For each heat map, the complete range of mean-centered node activities was used to generate the color range. The range of activity values in experiments that compared strains was at least 40 (−20 to 20), whereas the range of node 30 activities was much less in a data set in which only PAO1 or its derivatives were analyzed. (C) Pairwise percent sequence identities between orthologous genes from 13 P. aeruginosa strains. Two operons that contain the top 5 HW genes in node 30 were analyzed. HW genes are shown in red. (D) Phylogenetic trees of pilA (the most HW gene) and nadC (pilA’s immediate neighbor). The two trees share the same distance per branch length unit, and the longer branch represents more genetic changes. Jie Tan et al. mSystems 2016; doi:10.1128/mSystems.00025-15