Predector - supplementary material

All supplementary material and full resolution figures for the Predector pipeline manuscript.Figure 1: UpSet plot showing predictions of signal peptides, transmembrane domains, and effector-like properties for all known effectors in the training dataset (N=125). Rows indicate sets of proteins predicted to have a property related to effector prediction (e.g. a signal peptide), with the horizontal bar chart indicating set size. Columns indicate where the horizontal sets intersect with each other, where the vertical bar-chart indicates the number of proteins in that intersection. For clarity, intersections with only 1 member have been excluded, the full plot is presented in supplementary figure 1.Figure 2: A violin plot showing the distributions of Predector effector ranking scores for each class in the test and training datasets. The effectors consist of experimentally validated fungal effector sequences. “Secreted” and “non-secreted” proteins are manually annotated proteins from the SwissProt database. Proteomes consist of the complete predicted proteomes from 10 well studied fungi (Supplementary table 2). The number of proteins represented by each violin are indicated on the x-axis.Figure 3: Comparing the scores of Predector with EffectorP versions 1 and 2 for proteins in the testing dataset. Scatter plots in the lower-left corner indicate comparisons of predictive scores between methods, with predicted secreted proteins (any signal peptide and fewer than two TM domains predicted) indicated in yellow, and non-secreted proteins indicated in blue. Density plots along the diagonal indicate distributions of the full test dataset versus predictive scores for each method (indicated along the x-axis), also coloured by secretion prediction as before (Note: there are far more non-secreted than secreted proteins in the dataset). Scatter plots in the top-right corner indicate score comparisons between methods for confirmed effectors, coloured by whether they have been predicted as secreted (criteria as above), or additionally predicted by EffectorP versions 1 or 2. Two proteins that are misclassified by a Predector score > 0 are labelled in the top-right subplot.Supplementary Table 1: Examples of confirmed fungal plant pathogenicity effector proteins that do not exhibit the commonly targeted protein properties of low-molecular weight, cysteine-richness and presence of classical N-terminal secretion signal peptide.Supplementary Table 2. Datasets used for training and evaluation.Supplementary Table 3. Weights assigned for manual scores. Description of parameters used to calculate combined Predector scores, based on weight-adjusted values. Individual scores were determined by multiplying the value by weight, and the combined Predector score was calculated from the sum of all individual scores.Supplementary Table 4. Extended model evaluation and statistics.The supplementary figures document contains its own documentation.