Fig. 13

Summary of differentially expressed (DE) genes in Pcdh10-rescued PTD7_RL cells versus malignant Pcdh10-lacking PTD7 cells. The analysis was performed by the Ingenuity Pathway Analysis software (IPA, Qiagen) (see also Table 2). Details on this analysis can be found in https://qiagen.secure.force.com/KnowledgeBase/KnowledgeIPAPage and https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/. The top network score is based on a p-value calculation, which calculates the likelihood that the Network Eligible Molecules that are part of a network are found therein by random chance alone. The graphical summary below provides a coherent and comprehensible synopsis of the major biological themes in the IPA core analysis performed, including upstream regulators, diseases, functions, and pathways, and illustrates how those concepts relate to one another. The algorithm takes into account the magnitude of the differential expression of the corresponding gene in the dataset when deciding which regulators to include. In the left part, major DE genes are indicated in their subcellular compartment, with connecting lines indicating direct (solid lines), indirect (broken lines) or inferred (dotted lines) relationships. In the right part, molecular and cellular functions (octagons) influenced by Pcdh10 re-expression, as well as associated diseases (crosses) are listed. In an IPA core analysis, the z-score of a regulating molecule predicts the activation state of this upstream regulator, using the molecular expression patterns of the molecules downstream of an upstream regulator, being either increased for an activating gene or decreased for an inhibiting gene. Items with a positive z-score (activated) are colored orange (none in this summary), and those with negative z-score (inhibited) are colored blue. Network shapes, used here or in Additional file 24: Figs. S12-S17, include rectangles for cytokines, inverted triangles for kinases, horizontal ovals for transcriptional regulators, vertical rectangles for G-protein coupled receptors, and diamonds for non-kinase enzymes