The soybean defense response to the soybean cyst nematode was used as a model to map at cellular resolution its genotype-defined cell fate decisions occurring during its resistant reactions. The defense responses occur at the site of infection, a nurse cell known as the syncytium. Two major genotype-defined defense responses exist, the G. max[Peking]- and G. max[PI 88788]-types. Resistance in G. max[Peking] is potent and rapid, accompanied by the formation of cell wall appositions (CWAs), structures known to perform important defense roles. In contrast, defense occurs by a potent but more prolonged reaction in G. max[PI 88788], lacking CWAs. Comparative transcriptomic analyses with confirmation by Illumina® deep sequencing were organized through a custom-developed application, Pathway Analysis and Integrated Coloring of Experiments (PAICE) that presents gene expression of these cytologically and developmentally distinct defense responses using the Kyoto Encyclopedia of Genes and Genomes (KEGG) framework. The analyses resulted in the generation of 1,643 PAICE pathways, allowing better understanding of gene activity across all chromosomes. Analyses of the rhg1 resistance locus was also performed.