Journal: PLoS Genetics

Article Title: A pals-25 gain-of-function allele triggers systemic resistance against natural pathogens of C . elegans

doi: 10.1371/journal.pgen.1010314

Figure Lengend Snippet: A) qRT-PCR of select ORR and IPR genes. * = Gene belongs to ORR and IPR, # = Gene belongs to only IPR, $ = Gene belongs to only ORR. The results shown are fold change in gene expression relative to WT. **** p < 0.0001, *** p < 0.001, ** p < 0.01, * p < 0.05, One-tailed t-test. n = 4 independent experimental replicates, different symbol shapes represent the expression values for replicates performed on different days. Bar heights indicate mean values and error bars represent standard deviations. B) Upregulated genes in both pals-25(Q293*) jy111 and pals-25(Q293*) icb98 mutants have significant overlap with genes regulated by wild-type pals-22 and pals-25 . Hypergeometric test, RF = 34.5; p < 5.39e-243 and RF = 15.6; p < 1.994e-182 for pals-25(Q293*) jy111 and pals-25(Q293*) icb98 , respectively. C-D) Upregulated genes in pals-25(Q293*) jy111 mutants have significant overlap with the IPR and ORR. Hypergeometric test, IPR: RF = 46.9; p < 6.215e-64, ORR: RF = 41.1; p < 6.883e-144. E-F) Upregulated genes in pals-25(Q293*) icb98 mutants have significant overlap with the IPR and ORR. Hypergeometric test, IPR: RF = 21.8; p < 4.529e-60, ORR: RF = 21; p < 5.122e-148. G) Correlation of differentially expressed genes in pals-25(Q293*) jy111 and pals-25(Q293*) icb98 mutants with those expressed during pathogen infection and regulated by known activators of the IPR. Correlation of gene sets quantified as Normalized Enrichment Score (NES) as defined by GSEAPreranked module analysis . Blue indicates significant correlation of downregulated genes in pals-25(Q293*) jy111 or pals-25(Q293*) icb98 mutants with the gene sets tested, and yellow indicates significant correlation of upregulated genes in pals-25(Q293*) jy111 or pals-25(Q293*) icb98 mutants with the gene sets tested. Grey indicates no significant correlation ( p > 0.05 or False Discovery Rate > 0.25). GSEA analysis of 93 gene sets tested can be found in . H) WormCat analysis shows significantly enriched gene categories represented in upregulated genes of pals-25(Q293*) jy111 and pals-25(Q293*) icb98 mutants. Bold text indicates broad “Category 1” biological processes enriched while nested text indicates more specific “Category 2 or 3” processes enriched. p values were determined using Fisher’s exact test with Bonferroni correction from minimum hypergeometric scores calculated in the WormCat software. A summary of WormCat analysis can be found in .

Article Snippet: A heatmap of the GSEA analysis was produced using Prism 9 (GraphPad).

Techniques: Quantitative RT-PCR, Gene Expression, One-tailed Test, Expressing, Infection, Software

Journal: Evidence-based Complementary and Alternative Medicine : eCAM

Article Title: Combined Lipidomics and Network Pharmacology Study of Protective Effects of Salvia miltiorrhiza against Blood Stasis Syndrome

doi: 10.1155/2021/5526778

Figure Lengend Snippet: (a) Chemical similarity enrichment analysis plot. (b) Heatmap of Spearman's correlation between differential metabolites and biochemical parameters. (c) Summary plot of metabolic pathways associated with differential metabolites.

Article Snippet: The heatmap analysis was performed by using PRISM GraphPad 8.0.

Techniques:

Journal: Evidence-based Complementary and Alternative Medicine : eCAM

Article Title: Combined Lipidomics and Network Pharmacology Study of Protective Effects of Salvia miltiorrhiza against Blood Stasis Syndrome

doi: 10.1155/2021/5526778

Figure Lengend Snippet: (a) Heatmap based on the normalized raw abundance of differential metabolites. (b) Changed metabolites between the model group and the Danshen-treated group: green means significant difference ( p < 0.05), and red means no significant difference ( p > 0.05). CG: control group; MG: model group; PG: positive control group; DG: Danshen-treated group.

Article Snippet: The heatmap analysis was performed by using PRISM GraphPad 8.0.

Techniques: Control, Positive Control

Journal: International Journal of Molecular Sciences

Article Title: From High Protection to Lethal Effect: Diverse Outcomes of Immunization Against Invasive Candidiasis with Different Candida albicans Extracellular Vesicles

doi: 10.3390/ijms26010244

Figure Lengend Snippet: ( a ) Hierarchical heatmap depicting the relative abundance of each protein across the three different types of EVs, with darker shades of red indicating higher relative abundance (measured by NSAF) (protein names shown represent 1 out of every 22 proteins for clarity). ( b ) Zoomed-in view on the region of the heatmap with a higher abundance in cell surface proteins in SC5314 YEVs. Proteins described as immunogenic in the Candida Genome Database (CGD) are marked with an asterisk.

Article Snippet: The NSAF values, which are calculated considering the number of matched peptide spectra (PSMs) and the molecular weight, were used to conduct a clustering heatmap analysis with Rstudio ( a).

Techniques:

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