Figure 3. The cellular signatures of growth associated protein 43 (Gap43), retinal pigment epithelium-specific protein 65 kDa (Rpe65), and choline O-acetyltransferase (Chat) illustrated by quantitative trait loci (QTL) heat maps. The correlation matrices within GeneNetwork were used to simultaneous map and analyze the top 80 genes in the trait collections of A: Gap43, B: Rpe65, and C: Chat. The gene collections from Gap43, Rpe65, and Chat form unique signatures within the retina transcriptome. The numbers to the left denote the correlation range and at the bottom of the heat maps the chromosomal location is noted ranging from chromosome 1 on the left to chromosome X on the right. The banding pattern is displayed in yellow, red, green, and blue, which denote the locations of the genomic loci that modulate all of the genes in the network. The hues: yellow, red, green, and blue represent significant QTLs. The green (low LRS) to blue (high LRS) coloring represents transcripts whose expression is higher in the strains with a B haplotype (C57BL/6J) and the yellow (low LRS) to red (high LRS) coloring corresponds to the transcripts whose expression is higher in the strains with mutant D haplotype (DBA/2J). The red arrows indicate that some of the bands are more prominent. Running a QTL cluster map in GeneNetwork reveals a strong QTL signature of Gap43, forming a potential genetic network. Signature QTLs (highlighted with red arrows) for Gap43 were found on chromosomes 1, 2, 7, 12, 15, 16, and 19. These are regions of the genome that contain loci modulating the expression of genes within the Gap43 network (A). Rpe65 forms signature QTLs on chromosomes 1, 9, and 16 (B) and Chat forms signature QTLs on chromosomes 1, 5, 7, and 9 (C).