Fig. 1

Pipeline to determine candidate plasmodesmata (PD) proteome. a A flowchart explaining PIP1 approach is presented. Proteome data, determined experimentally by [2] (Proteome 1, P1), [3] (Proteome 2, P2), [5] (Proteome 3, P3) and [4] (Proteome 4, P4), were used. A list was compiled of subfamilies of proteins identified in P1-P4 using PANTHER16. Genes belonging to these subfamilies were extracted for the target plant species. These were classified by whether its subfamily was present in one or in two or more experimental proteomes. Predictions of encoding a signal peptide (SP), transmembrane domain (TM) or glycophosphatidylinositol anchor (GPI) were used to classify the genes as these features are enriched in verified PD proteins (see Additional file 1: Table S1). PIP1 outputs 4 list of genes (A-D) according to these classifications representing the in silico PD proteome for the target plant. b A Venn diagram showing the overlap between subfamilies identified in P1-P4 experimental proteomes (311 subfamilies appear in more than one proteome). See Additional file 1: Table S3