Fig. 1

Differential gene expression profile reflecting macrophage polarization in response to influenza A virus infection. a k-means clustering analysis of RNA-Seq counts using a Poisson-based distance metric. The final representative values in each cluster were normalized to the total library size for the purpose of visualization. b The estimated percentage of the M1 macrophage subtype in each sample as estimated by non-negative matrix factorization. 95% confidence intervals are denoted by the whiskers displayed around each point. c The relative pattern of expression of genes identified as strong M1 and M2 subtype markers based on RNA-Seq data. Each point represents the mean sample-wise rank of the top 1000 putative M1-associated genes (red) and top 1000 putative M2-associated genes (blue) based on the cell subtype coefficient estimated from the linear model applied to the RNA-Seq dataset