Extended Data Fig. 4. Differential cell type prioritization in single-cell RNA-seq data.
a, Schematic overview of the permutation-based test for differential prioritization with Augur. First, cell type prioritization is performed within each of two conditions separately, yielding condition-specific AUCs for each cell type. Next, sample labels are randomly permuted within each cell type, and cell type prioritization is performed on shuffled data, yielding a null distribution of AUCs for each cell type and condition. AUCs for matching cell types are compared across conditions to calculate a ‘ΔAUC score’ for each cell type, and a null distribution of ΔAUC scores is calculated using the permuted data. Permutation p-values can then be calculated for each cell type, enabling the identification of statistically significant differences in cell type prioritization between conditions, as well as the condition in which the cell type is more transcriptionally separable.
b, Neuron subtypes with statistically significant differences in AUC between female and male mice during parenting, in a single-cell imaging transcriptomics experiment employing multiplexed error robust fluorescence in situ hybridization (MERFISH)6 (n = 79 subtypes). Eleven subtypes have significantly higher AUCs in female parents, whereas two have significantly higher AUCs in male parents.
c, Relationship between differential prioritization ΔAUC for parenting between male and female mice, and AUC for sex in naive mice. Several neuronal subtypes preferentially activated during parenting in female mice are also transcriptionally distinct in naive mice, such as the I-32 cluster, which is enriched for aromatase expression, and expresses multiple sex steroid hormone receptors6.
d, Neuron subtypes with statistically significant differences in AUC in response to whisker lesioning in Cx3cr1+/− as compared to Cx3cr1−/− mice, in a single-cell RNA-seq experiment7 (n = 28 subtypes). Four subtypes are have significantly higher AUCs in homozygous mice, whereas one subtype has a significantly higher AUC in heterozygous mice.