Journal: Journal of Fungi

Article Title: Characterization and Functional Analysis of a New Calcium/Calmodulin-Dependent Protein Kinase (CaMK1) in the Citrus Pathogenic Fungus Penicillium italicum

doi: 10.3390/jof8070667

Figure Lengend Snippet: Transcriptome analysis of the differentially expressed genes (DEGs) between the control and Δ PiCaMK1 strains. ( A ) Clustering (heatmap) analysis of the DEGs. ( B ) Volcano plot analysis of the DEGs. ( C ) MA plot analysis of the DEGs.

Article Snippet: Software Plotly (Montreal, Quebec, QC, USA) was processed for heatmap analysis of hierarchically clustered unigenes with Venn diagram-based visualization.

Techniques: 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

Journal: Scientific Reports

Article Title: The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginica

doi: 10.1038/s41598-020-67851-4

Figure Lengend Snippet: In the heatmap analysis the vertical clustering indicates the similarity of the abundance between different genera. The shorter the distance between the two genera, the more similar abundance between the samples. In the horizontal clustering, the closer and shorter of the branch length between the samples, the more similarity of the abundance.

Article Snippet: “According to the taxonomic composition and relative abundance of each sample, the genera heatmap analysis was carried out to extract the species at each taxonomic level and plotted using the R language tools, the heatmap clustering analysis was conducted at the level of phylum, class, order, family, genus and species respectively” (CD Genomics).

Techniques: