Supplementary File 1: Protein Datasets Used in the TFG: P. infestans Secretome from Meijer et al 2014 and S. lycopersicum interactome The file includes 3 excel sheets: Sheet 2: Secretome of Phytophthora infestans from Meijer et al 2014: protein sequences H. J. G. Meijer et al., “Profiling the Secretome and Extracellular Proteome of the Potato Late Blight Pathogen Phytophthora infestans,” Mol. Cell. Proteomics, vol. 13, no. 8, pp. 2101–2113, 2014. Sheet 3: Interactome of Solanum lycopersicum from STRING database. Only physical interactions and score over 900: protein sequences Sheet 4: Interactome of Solanum lycopersicum from STRING database. Only physical interactions and score over 900: pairs of interactors
Supplementary File 2: Gene expression Pearson correlation between interacting predicted proteins (Target-Effector) and effectors that target the same host protein (Effector-Effector) This file contains the results of gene expression Pearson correlation for the best 30 interactions yielded by the 4 sets of results For each set of results, each line contains the pair of proteins involved, the Pearson coefficient and the Pearson P-value and the adjusted P-value
Supplementary File 3: This file contains the list of GO terms considered as infection related and the GO enrichment on the host predicted targets The list was build as the result of the GO annotation of the Solanum lycopersicum proteins of the known interactions found in Whisson et al 2016 Sheet 2: contains the GO terms enriched for each of the 4 result set as well as the inclusion or not of these GO terms in the lists of Infection related GO terms Sheet 3: contains the list of GO terms and their functions Sheet 4: list result of adding all children GO terms of the previous list
Figure S1: Best 30 predicted interactions for the S. lycopersicum – P. infestans pathosystem using only domains in the pipeline. Left: D set (not including cytoplasm). Right: DC set (including cytoplasm). Pathogen effectors are plotted as red triangles, host targets as black circles and the rest of host proteins as blue circles.
Figure S2: Best 30 predicted interactions for the S. lycopersicum – P. infestans pathosystem using also motifs in the pipeline. Left: DM set (not including cytoplasm). Right: DMC set (including cytoplasm). Pathogen effectors are plotted as red triangles, host targets as black circles and the rest of host proteins as blue circles.
Figure S3: Dyer (A) and Zhang (B) scores for STRING interactome and for negative interactome protein pairs using domains and motifs.
4BestInteractomes: File .cys (Cytoscape software). It contains the 4 Solanum lycopersicum - Phytophthora infestans best sets of interactions over the interactome of S. lycopersicum. Source of Figures S1 and S2.