kegg pathway enrichment analysis  (RStudio)

Journal: Nature Communications

Article Title: NMR and MS reveal characteristic metabolome atlas and optimize esophageal squamous cell carcinoma early detection

doi: 10.1038/s41467-024-46837-0

Figure Lengend Snippet: A Pie chart of quantified metabolite categories. Colors represent different compound super-classes; coloration follows the legend counterclockwise per each pie chart. B Volcano plot analysis performed on early-ESCC tissue samples vs. normal controls. P -values were determined by two-sided t -test without adjustments. Differentially-expressed metabolites are indicated by blue dots (down-regulation relative to normal controls) and red dots (up-regulation relative to normal controls), respectively. Gray dots indicate no significant difference. C Treemap of the most enriched KEGG pathways in early-ESCC tissue samples. Relative betweenness centrality was the selected node importance measure for pathway topological analysis. Each square represents a metabolic pathway; the square size represents the impact factor in the topological analysis; the color of the squares indicates the p -value of the enrichment analysis; and the darker the color, the more significant the enrichment. D O2PLS loading plots of the key differential metabolites analyzed by NMR-based and MS-based metabolomics. The top 30 metabolites in early-ESCC tissues detected by NMR and MS are labeled in purple and blue, respectively. Source data are provided as a Source Data file.

Article Snippet: KEGG metabolic pathway enrichment analysis was further performed (Fig. ), and we found that ‘Alanine, aspartate and glutamate metabolism’ consistently exhibited the most significant changes from tumor-bearing to tumor-resected phase and to healthy status in biofluids (Supplementary Fig. ).

Techniques: Labeling

Journal: Aging (Albany NY)

Article Title: miR-506-3p induces autophagy of renal tubular epithelial cells in sepsis through targeting PI3K pathway

doi: 10.18632/aging.204759

Figure Lengend Snippet: Bioinformatics analysis. ( A ) The gene expression in GSE101639 was subjected to quantile normalization. ( B ) DEGs in normal group and sepsis group. ( C ) It was found in GSE154918 that the expression of PIK3CA was down-regulated in sepsis compared with that in normal samples. ( D ) The upstream miRNAs of PIK3CA were evaluated through miRDB, starBase and TargetScan, and the DEG of miR-506, a key regulator of PIK3CA, was obtained from the intersection. ( E ) miR-506 of PIK3CA had a targeted binding region. ( F ) GO enrichment analysis was performed using the online tool DAVID. A total of 37 down-regulated pathways were enriched, including autophagy, transcription elongation from RNA polymerase II promoter and regulation of blood pressure. ( G ) 30 up-regulated pathways, including protein SUMOylation, glucose homeostasis and negative regulation of protein kinase activity. ( H ) KEGG pathway analysis was conducted on the integrated DEGs using DAVID. ( I ) The hub gene was obtained by Cytoscape.

Article Snippet: Furthermore, KEGG pathway enrichment analysis using R-Studio showed that miR-506-3p had a targeted regulatory effect on PIK3CA, a key gene in the PI3K-Akt signaling pathway.

Techniques: Gene Expression, Expressing, Binding Assay, Activity Assay