volcano plots and heatmaps  (Novogene)

Journal: Nature Communications

Article Title: Natural variation of an E3 ubiquitin ligase encoding gene Chalk9 regulates grain chalkiness in rice

doi: 10.1038/s41467-025-61683-4

Figure Lengend Snippet: a The genome-wide association signals for chalky grain rate (CGR) and degree of chalkiness (DC) in the region at 18–21 Mb on chromosome 9 ( x -axis) across two years. Negative log 10 -transformed P values from the linear mixed model are plotted on the y -axis. The horizontal dashed line indicates the genome-wide significance threshold ( P = 1×10 –6 ). P values were determined using a two-sided Wald test and assessed after Bonferroni correction for multiple comparisons. b Linkage disequilibrium (LD) heatmap of the Chalk9 locus region. Pairwise linkage disequilibrium was determined by calculating r 2 (the square of the correlation coefficient between SNPs). c Relative expression level of the 12 candidate genes in the endosperm of eight high-chalky and eight low-chalky varieties at 20 days after flowering (DAF). The 12 predicted genes in the Chalk9 locus region are labeled by I to XII. Data show means ± SD ( n = 8 varieties). P values were calculated for comparisons between high-chalky and low-chalky groups, with each group comprising 8 varieties. d Relative expression level of the candidate gene III ( Chalk9 ) in the endosperm from the selected varieties at 20 DAF. The P value was calculated for the comparison between high-chalky and low-chalky groups, with each group comprising 8 varieties. Data show means ± SD ( n = 3 biological replicates). e Relative expression level of the 12 candidate genes in the leaves of eight high-chalky and eight low-chalky varieties. Data show means ± SD ( n = 8 varieties). In c – e , statistical analysis between high-chalky and low-chalky groups was performed by two-tailed Student’s t -test. Source data are provided as a Source Data file.

Article Snippet: Correlation analysis, heatmap plotting, and volcano plot analysis were performed using BMKCloud ( www.biocloud.net ).

Techniques: GWAS, Transformation Assay, Genome Wide, Expressing, Labeling, Comparison, Two Tailed Test

Journal: Cancer Gene Therapy

Article Title: Dual-inhibition of NAMPT and PAK4 induces anti-tumor effects in 3D-spheroids model of platinum-resistant ovarian cancer

doi: 10.1038/s41417-024-00748-w

Figure Lengend Snippet: A PCA showing gene profiles of 3D-cultured CP80 after treatment with KPT-9274 1000 nM for 24 h relative to Control. (Results shown are from four independent experiments). B Heatmap representing DEGs in treated 3D-cultured CP80 as described above. (Cutoff used: p < 1e-5). C Volcano plot generated to identify DEGs in 3D-cultured CP80 after KPT-9274 treatment relative to Control. (Cutoff used: |Difference (Log 2 Fold Change) of group means | >1, and -Log 10 ( p -value) >1). D Left: Normalized enrichment score of various gene sets in Control group relative to KPT-9274 treatment are shown in bar plots. Right: GSEA in Control group relative to KPT-9274 treatment. (Top: Hallmark gene sets in MsigDB, bottom: KEGG pathway DB). E Top: Pathways affected by KPT-9274 treatment as identified by Ingenuity pathway analysis (IPA). Bottom: Normalized gene expression levels associated with Interferon Signaling in Control and KPT-9274 treatment. ( n = 4 independent experiments). F Top: Immunoblotting for assessing the expression of IFNGR1, IFIT1, and IFITM2/3 in 3D-cultured CP80 cell lysates with KPT-9274 treatment at indicated doses. GAPDH and LaminB1 were shown as controls. (Left: cytoplasm lysate, Right: nuclear lysate) Bottom: Cytoplasmic protein levels normalized by GAPDH in Control and KPT-9274 treatment. ( n = 4 independent experiments). G Schematic showing that KPT-9274 inhibits Wnt/β-Catenin signaling by reducing the expression of inflammatory-related proteins, including IFNGR1 and IFIT1. Graph data were presented as mean ± SEM with n = 4 per group.

Article Snippet: To identify Differentially Expressed Genes (DEGs), heatmap and volcano plot were created with Qlucore omics explorer (ver.

Techniques: Cell Culture, Control, Generated, Gene Expression, Western Blot, Expressing