pca expression plot feature  (RStudio)

Journal: bioRxiv

Article Title: Persistent interferon signaling and clonal expansion mark early events in DNA methylation damage-induced liver cancer

doi: 10.1101/2025.10.01.679856

Figure Lengend Snippet: a , Whole-cell liver lysates collected at 1 day, 5 days, and 10 weeks post-exposure were analyzed by western blot for phosho-p53. Band intensities normalized to TPS and saline WT controls. n = 4 per group (2 males, 2 females). b , Liver lysates from identical timepoints were immunoblotted for p21, normalized as above. n = 4 per group (2 males, 2 females). c , Liver lysates from identical timepoints were immunoblotted for RAD51, normalized as above. n = 4 per group (2 males, 2 females). d , e , Principal Component Analysis (PCA) of phosphoproteomics at 1 day ( d ) and 10 weeks ( e ) post-exposure displayed distinct sample clustering by treatment group and genotype. n = 4 (2 males and 2 females). f , g , Heatmaps show the most differentially expressed phosphorylated proteins at 1 day ( f ) and 10 weeks ( g ) post-exposure, identified by phosphoproteomics. DNA repair proteins are highlighted in bold ( f ). Protein selection based on multi-group ANOVA by treatment (p < 0.05), with standard deviation < 0.05; 354 total proteins ( f ), 214 total proteins ( g ). h , Phosphoproteomic quantification of gH2AX (combined S140 and S137 sites) at 1 day post-exposure. n ≥ 2 per group. i, STRING database analysis of top-expressed phosphoproteins at 1 day and 10 weeks post-exposure. Functional enrichment at 1 day highlights DNA repair clusters; 10 weeks displays enrichment for non-DNA repair biological processes from gene ontology. Statistical comparisons performed using one-way ANOVA with Šídák’s multiple comparisons test ( a – c , h ). Data are presented as mean ± s.e.m. Statistical significance: *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. NS, not significant.

Article Snippet: Qlucore software was used to generate heatmaps and PCA plots.

Techniques: Western Blot, Saline, Phospho-proteomics, Selection, Standard Deviation, Functional Assay

Journal: bioRxiv

Article Title: Persistent interferon signaling and clonal expansion mark early events in DNA methylation damage-induced liver cancer

doi: 10.1101/2025.10.01.679856

Figure Lengend Snippet: a , PCA of Mgmt −/− liver samples collected at days 1, 2, and 5 post-saline or NDMA exposure shows clear clustering separation by treatment group. RNA was extracted from liver tissue and analyzed by RNA-seq; n ≥ 7 per group (males and females combined). b , Bar graphs depict the number of differentially expressed RNA transcripts (up- and downregulated) in WT and Mgmt −/− liver following NDMA exposure across indicated timepoints. c , Venn diagrams compare overlap of significantly up- and downregulated genes across genotypes and timepoints. d , Pathway enrichment analysis of persistently up- and downregulated genes (intersected across all timepoints from panel c , red circles) in Mgmt −/− samples using Enrichr for MSigDB Hallmark gene sets. The top 8 pathways are displayed, ranked by Fisher exact test p-value. Pathways involved in IFN response are marked with an asterisk (*). e , Volcano plots display the most differentially expressed genes in Mgmt −/− livers comparing NDMA vs saline treatment at 1 day, 5 days, and 10 weeks. Plots show –log 10 p-value versus log 2 fold change. Genes from the GSEA Hallmark p53 pathway are circled in red or black; Cyp2e1 downregulation is circled in blue. f , i , Bar graphs quantify the number of up- and downregulated genes within the pre-curated IFN ( f ) and DNA repair ( i ) gene lists, comparing NDMA effects between WT and Mgmt −/− across the time course. g , h , Heatmaps show expression profiles for curated IFN response genes ( g ) and DNA repair genes ( h ) in response to NDMA treatment in WT and Mgmt −/− livers at days 1, 2, and 5 post-exposure. Color scale reflects relative gene expression intensity. Statistical analysis: All comparisons use thresholds of adjusted p-value < 0.05 and absolute log 2 fold change > 0.58 ( b – i ).

Article Snippet: Qlucore software was used to generate heatmaps and PCA plots.

Techniques: Saline, RNA Sequencing, Expressing, Gene Expression

Journal: Poultry Science

Article Title: Molecular mechanisms of photoperiod regulation of bile acid metabolism in Taihe silky fowls based on the gut-liver axis

doi: 10.1016/j.psj.2025.105489

Figure Lengend Snippet: Effect of photoperiod on serum bile acid profile in Taihe silky fowls. (A) PCA plot; (B) Bile acid clustering heatmap; (C) Bar chart of differentially abundant bile acids fold changes; (D) KEGG enrichment plot of differentially abundant bile acids. Data are presented as means ± SEM ( n = 6).

Article Snippet: Effect of photoperiod on serum bile acid profile in Taihe silky fowls. (A) PCA plot; (B) Bile acid clustering heatmap; (C) Bar chart of differentially abundant bile acids fold changes; (D) KEGG enrichment plot of differentially abundant bile acids.

Techniques:

Journal: Poultry Science

Article Title: Molecular mechanisms of photoperiod regulation of bile acid metabolism in Taihe silky fowls based on the gut-liver axis

doi: 10.1016/j.psj.2025.105489

Figure Lengend Snippet: Effects of photoperiod on liver gene expression in Taihe silky fowls. (A) PCA plot; (B) Bar chart of differentially expressed genes; (C) Volcano plot of differentially expressed genes; (D) GO enrichment analysis bubble plot of differentially expressed genes; (E) KEGG enrichment analysis bubble plot of differentially expressed genes. Data are presented as means ± SEM ( n = 3).

Article Snippet: Effect of photoperiod on serum bile acid profile in Taihe silky fowls. (A) PCA plot; (B) Bile acid clustering heatmap; (C) Bar chart of differentially abundant bile acids fold changes; (D) KEGG enrichment plot of differentially abundant bile acids.

Techniques: Gene Expression

Journal: Scientific Reports

Article Title: A bioinformatics-driven approach to identify biomarkers and elucidate the pathogenesis of type 2 diabetes concurrent with pulmonary tuberculosis

doi: 10.1038/s41598-025-00928-0

Figure Lengend Snippet: Comparative bioinformatic analyses of immune cell enrichment in the PTB + T2DM and HC groups. ( A - B ) Enrichment scores of 22 distinct immune cell types in the two groups (PTB with T2DM vs. Healthy control and PTB with T2DM vs. T2DM group). ( C ) Correlation analysis between six key genes in PTB + T2DM and various immune cell types. ( D ) PCA was performed using the PCA expression plot feature in RStudio, data dimensionality of the data set was reduced, allowing the creation of a two-dimensional scatter plot for an initial sample distribution assessment. ( E ) Spearman’s correlation analysis of C1QA and LINC00278 expression with M2 macrophages. The values on the x-axis represent the relative enrichment level of M2 macrophages, and the values on the y-axis represent the expression levels of C1QA and LINC00278.

Article Snippet: Healthy control and PTB with T2DM vs. T2DM group). ( C ) Correlation analysis between six key genes in PTB + T2DM and various immune cell types. ( D ) PCA was performed using the PCA expression plot feature in RStudio, data dimensionality of the data set was reduced, allowing the creation of a two-dimensional scatter plot for an initial sample distribution assessment. ( E ) Spearman’s correlation analysis of C1QA and LINC00278 expression with M2 macrophages.

Techniques: Control, Expressing