Figure 5.

High-dimensional gene expression analysis reveals novel SCN cell-types. (A) Neuron correlation network based on Pearson correlation analysis across the multi-genic (87 genes) transcriptional states of the light-pulsed neurons. Each node represents an individual light-treated neuron. Edges indicate positive Pearson correlation coefficients >0.5. Highly interconnected groups of neurons, representing community structures within the correlation network, are labeled and colored accordingly. A fifth group of neurons (representative gray node) showed little or no correlations with other neurons. Genes listed next to each group correspond to the five genes with the highest number of correlations with the other genes (across cells) within the defined neuronal group. (B) Heat map visualizing the underlying transcriptional states corresponding to the SCN neuronal subtypes identified in (A). (C) MDS 2-dimensional plot of light-treated neurons, similar to Figure S10C, with new neuronal group annotation (A). Using this new neuronal group annotation, distinct clusters are apparent, with the exception of Group 5 neurons that are scattered throughout the plot which reflects some of the similarities that these neurons share transcriptionally to the neurons of the other groups. Silhouette scores for the neuronal groups were calculated to be: Group 1 (0.554), Group 2 (0.239), Group 3 (0.321), Group 4 (0.324), Group 5 (−0.258).