We next compared the gene expression levels for the probes expressed by both RGCs and amacrine cells at different ages (
Fig. 5A). Since the absolute gene expression levels for amacrine cells and for RGCs are on different, arbitrary scales, we converted absolute gene expression levels to ranked gene expression levels for each cell type, assigning the gene with the highest amacrine cell expression at a given age a rank of 1, and continuing down to a rank of 10,525 for E20, 10,574 for P5, and 10,502 for P11 (the number of genes present at each of those ages) and repeated the process for the RGC genes. Since RGCs expressed fewer genes at every age than did the amacrine cells, the RGC rank list was scaled to 10,525 for E20, and so on, to match the length of the amacrine cell gene list. The genes “present”
only in amacrine cells were given terminal rankings (e.g., 10,526) in RGCs, and vice versa, at each age. We then compared the ranked expression for each gene between the amacrine cells and the RGCs, to create a simple index. The average of the differences between rankings of amacrine cells and RGCs compared at E20, P5, and P11 of all the probes within a given gene ontology is shown in
Figure 5B, where the scale shows genes ontologies with genes that are more highly expressed in RGCs at one end and more highly expressed in amacrine cells at the other end. For example, RGCs at all ages expressed higher levels of genes within the
neurotransmi- and
immune ontologies (
Fig. 5B, top;
Table 2). This difference could be because amacrine cells secrete a variety of neurotransmitters and RGCs only a few but at higher levels, thus demonstrating greater differences in gene expression rankings.
2,38–40 On the bottom of
Figure 5B, amacrine cells expressed higher levels of genes in the categories
chromatin,
DNA, and
transcription. The index identified differences between amacrine cells and RGCs that were largely consistent across E20, P5, and P11 ages in most ontologies, except for a few ontologies such as
polarity,
neurit-,
chromosome, and
neurotransmi- which demonstrated greater developmental variability across this age range between these two neuron types.