Fig. 6: Mapping the P. aeruginosa cell surface with Phage-seq.
From: Bacterial cell surface characterization by phage display coupled to high-throughput sequencing
a, b First 3 principal components (truncated single value decomposition [TSVD]) of VHH relative abundance matrix at final round of selection. Each point represents a distinct selection or biological replicate, or a sample of the non-panned input library. a Selections (or library) colored according to growth condition. b Selections (or library) colored according to the category of antigen targeted by the selection. c Canonical correspondence analysis (CCA) of selections and a subset of the antigen matrix. CCA projects samples (selections) and features (antigens) into the same lower-dimensional space. Antigens are depicted as vectors from the origin, and selections are shown as points. Each plot depicts the same 3D space with a different antigen vector and cells positive for that antigen highlighted in separate panels. Left, flagellar hook-basal body; center, OprM; right, type III secretion system (T3SS). d–g For each antigen shown in Fig. 3c with > 10 example selections, a classifier was trained to predict whether that antigen was present or absent in the relevant selection. Repeated stratified 5-fold cross-validation was performed and area under the receiver-operator characteristic curve (AUROC) was calculated for each antigen. As a control, classifiers were fit against the same selections with the labels randomly permuted. Trained classifiers were used to predict whether each antigen was present or absent for all samples in the selection. \(p\)-values, Wilcoxon rank-sum test (one-sided; H1: AUROC > 0.5). Source data are provided as a Source Data file. EPS Exopolysaccharide, LPS lipopolysaccharide, QS quorum sensing.
