Figure 1.

Genome-wide comparative transcriptome analysis of ST1275 under different pH, temperature and milk base. (A) Heatmap of gene expression level for samples collected from 4 conditions; genes are retained if they are expressed at a count-per-million (CPM) above 0.5 in at least two samples; expression values are normalized log₂CPM by using edgeR package. (B) visualization of expression profiles (log₂CPM) of different samples by multi-dimensional scaling (MDS) plot in edgeR package. (C) visualization of expression profiles (log₂CPM) of different samples by principal component analysis (PCA) plot in ggfortify package. (D) Detection of DEGs for samples from condition 2 compared to samples from condition 1. (E) Detection of DEGs for samples from condition 3 compared to samples from condition 2. (F) Detection of DEGs for samples from condition 4 compared to samples from condition 2. Genes with a fold-change significantly above 1.0 at an FDR cut-off of 5% is considered as DEGs. COG denotation: C, energy production and conversion; D, cell cycle control, cell division, chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; n.a., not assigned; O, post-translational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms; X, mobilome: prophages, transposons.