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. 2021 Nov 5;12:771691. doi: 10.3389/fphys.2021.771691

FIGURE 2.

FIGURE 2

DOX-responsive transcriptomic changes in mIMCD3 cells. (A,B) Identification of transcriptomic changes in mIMCD3 cells treated with DOX for 3 and 6 days using RNA-Seq-based differential expression analysis. Significantly changed genes (FDR < 0.05 over 20% expression change threshold) were labeled as green in volcano plots and used further downstream analysis. (C) Gene Ontology (GO) biological processes significantly enriched by DOX-responsive genes. Cellular processes (GO Biological Process) were identified from significantly changed genes by DOX treatment for 3 and 6 days. To avoid sample-source bias, whole transcriptome was used as a background gene set. Significant enrichment was considered as q < 0.05. (D) Bubble chart view of the GO term association using NaviGO. In the plot, the X-axis is the Resnik semantic similarity score (RSS) and the Y-axis chosen is Lin’s similarity score (LSS). GO terms are colored according to time point when DE genes are found, day 3, pink; day 6: green; and day 3 and 6: blue. The number of GO terms are listed in (C). (E) Heatmap of gene sets associated with “cell proliferation/differentiation” and “immune responses.” Full list of genes associated with GO terms are provided in Supplementary Table 4.