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Fig. 1 | BMC Gastroenterology

Fig. 1

From: CD10 and Das1: a biomarker study using immunohistochemistry to subtype gastric intestinal metaplasia

Fig. 1

Gene expression analysis of IM samples in patients without cancer (IM-GC). A Heatmap showing unsupervised clustering of samples using ALPI, CD24, CDX1, CDX2, MME, and MUC12 to subgroup samples (n = 14). Expression levels have been standardised (centered and scaled) within rows for visualization. Legend shows z score. Cluster 1 represents complete IM and cluster 2 represents incomplete IM samples. Samples S8 and S12 were removed from these 2 clusters as they likely represent mixed IM. B Volcano plot showing differentially expressed genes (logFC > 0.6 or < − 0.6 with FDR adjusted p < 0.05) between complete and incomplete IM. Probes with no gene names and differentially expressed probes/genes with duplicates removed. C Bar plot showing KEGG pathways [34] enriched in molecularly subtyped complete IM using single sample gene set enrichment analysis (ssGSEA). To calculate statistical significance, the Wilcoxon rank sum test followed by multiple test correction (Benjamini–Hochberg method) was used. No enriched pathways were detected in incomplete IM. Differential gene expression and ssGSEA were performed using the limma and GSVA packages in R

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