Extended Data Fig. 11: Comparison of mouse and human gene expression profiles in homologous lung cell types and across age.
From: A molecular cell atlas of the human lung from single-cell RNA sequencing
a, Scatter plots showing median expression levels (ln(CPM + 1)) in indicated cell types of each expressed human gene and mouse orthologue (mouse and human SS2 datasets, human and mouse cell numbers given in Supplementary Tables 2 and 6, respectively). Note tens to hundreds of genes that show a 20-fold or greater expression difference (and P < 0.05, MAST) between species (red dots, gene names indicated for some and total number given above). Basophil/mast cell 1 (Bas/Ma 1) cells have the most differentially expressed genes (343), and CD4+ M/E T cells have the least (79). Pearson correlation scores (R values) between the average mouse and human gene expression profiles for each cell type are indicated. ‘Mm()’ and ‘Hs()’ denotes genes in which duplications between mouse and human were collapsed to HomologyID. b, Heat map showing global transcriptome Pearson correlation between indicated human and mouse epithelial cells (SS2 dataset, human and mouse cell numbers given in Supplementary Tables 2 and 6, respectively). Red outline denotes homologous cell types based on classical markers described in Supplementary Table 6. White dot denotes human-to-mouse correlation. c, Dot plot of expression of canonical goblet cell markers MUC5B and MUC5AC and transcription factor SPDEF in mouse (left) and human (right) goblet cells. d, Scatter plot showing average expression levels (dots) across all cells (‘pseudo-bulk’ lung expression) of each expressed human gene and mouse orthologue (mouse and human SS2 datasets). Scale, ln(CPM + 1). Pearson correlation (R values) between the average mouse and human gene expression profiles are indicated. e, Scatter plots comparing median expression levels (ln(CPM + 1)) in indicated mouse lung cell types of each expressed gene at age 3 months (x axis) and 24 months (y axis) in SS2 datasets from Tabula Muris Senis40 (cell numbers given in Supplementary Table 6). Pearson correlation scores between average gene expression profile for each cell type at each age are indicated (R values), along with number of genes (red dots) showing 20-fold or greater expression difference (and P < 0.05, MAST) between ages. Names of some genes are given next to the corresponding red dot. For more details on statistics and reproducibility, please see Methods.
