Fig. 3

Co-expression analysis between PIP1 candidates and PD verified genes. A. thaliana co-expression data was extracted from ATTED-II database [52] and clustered based on hierarchical clustering (k = 151). a Cluster 87 and b cluster 100 show significant over-representation in verified subfamily members, PIP1-A and PIP1-C in relation to the whole ATTED-II database. Number underneath each bar = number of genes included within that cluster. Bars with differing letters above are significantly different (Fisher’s exact test, Holm corrected, p ≤ 0.05). c Clusters 87 and 100 represented using Cytoscape [53] where edge opacity was set to represent the degree of correlation between genes. Correlations <5.0 were filtered out. Node colour was set to represent candidates in PIP1-A (purple), PIP1-C (pink) and verified PD genes (green). Rhomboid shape are genes encoding proteins related with callose metabolism (manually curated). d Sub-network generated by selecting ‘first and second neighbours’ of callose- regulators BG_PPAP, PDLP2 and PDCB1 which map within the interactome region marked with discontinuous lines in c. Genes are listed in Additional file 1: Table S6