PAH-pollution effects on sensitive and resistant embryos: Integrating structure and function with gene expression
Fig 4
Differentially expressed genes (p < 0.01) during four critical developmental stages among sensitive and resistant embryo populations exposed to clean and polluted sediment.
Each row represents the embryo, treatment, and developmental stage; each column represents a gene. Clusters of genes with similar expression patterns relative to embryo treatment groups and developmental stage are shown on the left (gene tree). (A) Heat map and hierarchical clustering of significant genes (mixed model ANOVA, p < 0.01) in treatment-by-population-by-stage analysis of sensitive and resistant embryos exposed to clean and polluted sediment extracts. Expression of 6,789 genes was analyzed during four critical developmental stages—early somitogenesis (stage 21), heartbeat initiation (stage 25), late organogenesis (stage 31), and prehatching (stage 35)—of two F. heteroclitus embryo populations. Hierarchical clustering of the 114 genes with a significant treatment-by-population-by-stage interaction reveals four main clusters among treatment groups based on the similarities in gene expression patterns. Red indicates high expression levels and green represents low expression levels. (B) Heat maps and hierarchical clustering of genes whose expression significantly differs (pairwise comparisons, p < 0.01) within each developmental stage among sensitive and resistant embryos exposed to clean and polluted sediment extracts (CC, CP, PC, PP). The highest total number of significantly differently expressed genes (308) is at stage 35, while the lowest number of significantly differently expressed genes (77), is at stage 25. Red indicates high expression levels and green represents low expression levels. Cluster labeling shows five major clusters (highlighted by colors) of Stage 35 analyzed in the Discussion section.