Potential effect on molecular pathways in different targeted genes in the VEGF family in retina - From the genomic point of view

Abstract

This study's goal is to determine similarities and differences in the molecular pathways or potential functions of the various targeted regions or genes of the Vegf family—VegfA, VegfB, VegfC, and Pgf—using the BXD genetic reference panel. Data from whole genome expression profiles of retinas from the well-characterized mouse recombinant inbred (RI) strain population derived from C57BL/6J X DBA/2J (BXD) were analyzed. Multiple analytical tools and statistical strategies were used to investigate the expression level. The expression Quantitative Trait Loci (QTLs) of these probes were mapped and compared. Our data showed that VegfA2 has the highest expression levels among all probes of Vegf genes. The expression levels of Vegf family genes are not significantly correlated. In the overall comparison, expression levels of VegfA1 and VegfA2 are positively correlated (R = 0.540). The expression levels of VegfB and VegfC are weakly correlated (R = 0.360). VegfC is also weakly correlated with the expression levels of Pgf (R = 0.324). The interaction of VegfB- and VegfA2-associated 50a2 genes was very weak (R50 ab = 0.3129). The interaction of top VegfB-associated 50b genes with VegfA2 has a reciprocal negative impact (R50ba = −0.42758). The VegfC-associated top 50c genes are strongly correlated with VegfB (R50 cb = 0.8159), while they are negatively correlated with VegfA2 (R50ca = −0.1450). Expression quantitative trait loci (eQTL) analysis suggested that the regulatory mechanisms for the expression levels of these genes in the Vegf family are different from each other. The expression level of VegfA associates with a group of genes that are not associated with other genes in the Vegf family.