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Fig. 2 | BMC Medicine

Fig. 2

From: Sequential gene expression analysis of cervical malignant transformation identifies RFC4 as a novel diagnostic and prognostic biomarker

Fig. 2

Integrated analysis. A Principal component analysis of the most variable 1000 genes in three datasets. The first two principal components are displayed and colored according to the disease stage. The shaded ellipses represent the 95% confidence intervals. B Boxplots representing Pearson correlation coefficient distribution between cases at each stage. Kruskal-Wallis test followed by pairwise Wilcoxon rank-sum test with Bonferroni correction was used to compare correlations. *** p < 0.001. C Heatmap displaying Pearson correlations between pairwise comparisons for all samples. D Bar plot representing the number of DEGs in each disease stage across discovery datasets. E UpSet diagrams showing the intersection size of DEGs in HN and CN across discovery datasets. The colors of the matrix background represent up- (red) and downregulated (blue) genes. Orange bars represent the number of DEGs explained by unique genes to GPL570. Pale violet-red dots indicate inconsistently changed genes among different studies. F Venn diagram showing the number of shared and unique genes annotated in GPL96, GPL570, and GPL571. G Circos plot illustrating landscape of chromosomal positions, expression, CNVs, and significant chromosomal bands. Autosomes 1–22 and sex chromosome X are shown in the right half of the circle. Zoomed chromosomes 1, 3, and 19 are displayed in the left half. Tracks from innermost to outermost: expression heatmap of Sets1 genes along lesion severity gradient (LN-HN-CN, Track 1-3), frequency of gains (red), and losses (blue) for regions of each chromosome from TCGA-SCC (Track 4), chromosome cytobands (Track 5), and significantly enriched cytobands in zoomed chromosomes (Track 6). H Dot plot showing the results of cytoband enrichment. Dot color indicates the q-value of the enrichment test; dot size represents the fraction of genes annotated to each cytoband. Q-value < 0.05 is considered as statistically significant

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