Supplementary Figure 3: Dimensionality reduction of thalamic gene expression data.
From: A repeated molecular architecture across thalamic pathways
a. Scree plot of the PCA from Fig. 2 (22 nuclei, n=120 samples) shows the variance explained by the top 10 PCs compared to a shuffled matrix with the order of samples permuted for each gene (mean and standard deviation from 1000 permutations). The variance explained by the first 6 PCs is substantially larger than PCs of shuffled data. b. Dot plot illustrating separation of the three major profiles of thalamic projection neuron (primary, secondary, tertiary) along the first principal component (PC1). Thalamic nuclei are ordered by their mean position on PC1. Dots represent samples. c. Multidimensional scaling using an alternative distance metric also identifies a similar leading axis of variance with classical relay nuclei on one end and midline/intralaminar nuclei on the other end. Distance was defined as the quadratic mean of the log2 fold changes of the top 500 differentially expressed genes between any two samples (meaning that the gene set used for the distance comparison varies between each sample pair).
