Fig. 3

Heatmap showing differentially regulated genes in the nodal pathway related to cell cycle metaphase check point (cluster 1). Differentially expressed genes were analyzed using the “Pathway Maps” ontology and the top 50 most enriched pathways (PW) were identified. We clustered nodal PWs based on their gene content and reduced duplication. Complete linkage hierarchical clustering on the Jaccard distance between the complete set of genes in each PW was done and closely related individual entities were identified. Each cluster of closely related PWs was considered as one unit or mega pathway (dissimilarity cut off of 0.6). All associated differential genes were combined for creating heatmaps and analyzing gene interactions. Clustering of pathways has been detailed in Additional file 2: Table S2. The color key ranging from dark blue to dark red shows the degree of differential regulation from −2 of down regulation or more to +2 of upregulation or more. The color key ranging from dark blue to dark red shows the z-scored normalized expression level. This heatmap depicts the biological nodal pathway showing differential regulation of genes among the 4 different groups such as WT neonatal mice exposed to room air (WT RA), hyperoxia (WT HO), Sphk1 ^−/− mice exposed to room air (SK RA), or Sphk1 ^−/− mice exposed to hyperoxia (SK HO). Selected genes depicted in the heat map is described here. Among the genes prominently downregulated by hyperoxia in the WT include 1) centromere associated proteins, Cenp A, E, F and H, 2) Kinetochore proteins Bubr, Aurora A and B, Bub1 and Zwilch and 3) protein kinases such as Nek2a