R insight in to the function of DEGs. As shown in Figure

R insight into the function of DEGs. As shown in Figure 3D, overexpression of hub DEGs (CD38, CDMK2, TBC19) was very enriched in pathways associated to TStatistical AnalysisQuantitative outcome information are presented as signifies SD. Statistical evaluation was carried out with Student’s t-test or one-way analysis of variance in GraphPad Prism software. Statistical significance was set at p 0.05.Benefits Identification of Mitochondria-Related DEGs and Functional Enrichment Evaluation in pSSIn this study, 3 publicly available datasets–GSE40611, GSE127952, and GSE154926–which contained 17, eight, and 43 sufferers with pSS were used as education datasets. In addition, the GSE173808 dataset which incorporates 39 sufferers with pSS was appliedFrontiers in Immunology | frontiersin.orgMarch 2022 | Volume 13 | ArticleLi et al.Mitochondrial Dysfunction in PSSABCDEFEHFIGURE 2 | The heat maps, Venn diagram, and volcano plot of mitochondria-related-DEGs and gene-set enrichment analysis (NCBI-GEO database).SHH Protein Gene ID (A) The heat maps showed overlapping DEGs determined by the MitoMiner database which have been extracted from three publicly accessible GEO datasets by unsupervised hierarchical clustering within 3 groups.Endosialin/CD248 Protein MedChemExpress R-package heatmap was utilized for figure generation.PMID:23903683 (B, C) Venn diagrams showed the amount of upregulated (B) and downregulated DEGs (C) for every dataset as well as the number of genes that overlap in between them. (D) Volcano plot showed mitochondria-related DEGs (two instances of intersection) among pSS and controls. (E, F) The KEGG pathway analyses of upregulated (E) and downregulated DEGs (F) were performed with R package clusterProfiler and GSEA according to MSigDB C2-curated KEGG gene sets. (G, H) GO evaluation of upregulated (G) and downregulated (H) mitochondria-related DEGs was performed to identify enriched biological method like molecular function, cell component, and categories.Frontiers in Immunology | frontiersin.orgMarch 2022 | Volume 13 | ArticleLi et al.Mitochondrial Dysfunction in PSSABCDFIGURE three | Identification and validation of mitochondria immune-related hub genes. (A) Top rated: expression analyses in the eight mitochondria-related genes (CD38, CMPK2, ITIF3, LAP3, TBC1D9, XAF1, PYCR1, and SERHL2) in standard and pSS patient cohorts had been illustrated making use of the R package “ggpubr” function (p 0.001, Wilcox test) (NCBI-GEO database). Bottom: above genes identified by quantitative real-time PCR from our own cohort. Data shown were normalized to Actin expression and have been relative to expression in the non-pSS (n = 3, error bars represent mean SD, p 0.05, and p 0.01 by Student’s t test). (B) Heatmap shows Spearman correlation in between hub genes and immune cells. (C) The lollipop chart of CD38, CMPK2, TBC1D9, and PYCR1 demonstrates the correlation among genes and immune cells, an extension of Figure 4B. Lollipop size corresponds to the strength of this correlation. (D) Gene Set Enrichment Analysis (GSEA) of KEGG pathway enrichment for CD38, CMPK2, TBC1D9, and PYCR1 high-expression group versus low-expression group.cell/B cell receptor signaling pathways, key immunodeficiency, NK cell-mediated cytotoxicity, cytokine ytokine receptor interaction, along with the JAK/STAT signaling pathway (p 0.05). The pathways altered by PYCR1 were involved in the T cell receptor signaling pathway (p 0.05, FDR 0.079), cytokine ytokinereceptor interaction (p 0.01, FDR 0.049), and also the JAK/STAT signaling pathway (p 0.01, FDR 0.051) (Supplemental Table S4). Interestingly, the GSEA benefits confirmed a stron.