Fig. 3: RNA-seq analysis between TB and 2D culture.

a A heatmap of the differential gene expression. Red indicates high expression, and blue indicates low expression. b Volcano plot to identify genes that had a log2(fold-change, FC) value > 1 or <−1 and p < 0.05. c GO enrichment plot of the differential significantly expressed genes. The red box is related to angiogenesis terms, the blue box is related to hypoxia terms, and the green box is related to ECM remodeling terms. d KEGG enrichment plot of the pathway. The blue box is related to the hypoxia pathway. e Correlation heatmap of differential genes with angiogenesis. f Analysis of noteworthy genes. Fragments Per Kilobase per Million (FPKM). n = 3. To identify genes with significant changes in expression levels, we start by standardizing readcount. Next, we calculate the p value using the negative binomial distribution for hypothesis testing. Finally, we use Bonferroni correction to obtain the adjusted p value (padj). For bar graphs, data are presented as mean ± SEM. A two-tailed t-test was employed to compare two groups, followed by multiple comparisons with Bonferroni correction. Source data are provided in NC._data_file_s1.