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:

Journal: Cell Death Discovery

Article Title: Downregulation of phosphoglycerate mutase 5 improves microglial inflammasome activation after traumatic brain injury

doi: 10.1038/s41420-021-00686-8

Figure Lengend Snippet: Total 55,450 genes of cortical tissues were detected by LC Sciences for RNA-seq analysis. A GO enrichment analysis was carried out to classify the biological function of DEGs. Each box shows the GO term number, the p-value, and GO term. B KEGG pathway enrichment analysis for DEGs. The top 20 KEGG pathways are shown. The box color indicates the level of statistical significance. The dot size means the gene number. C A 1076 genes associated with inflammatory response were isolated and analyzed by VolcanoPlot. D Heatmap analysis of inflammation-related DEGs between WT group, WT TBI group, Pgam5 −/− group, and Pgam5 −/− TBI group. Only the top 40 genes were included in the DEGs heatmap.

Article Snippet: The Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Heatmap analysis, and VolcanoPlot analysis were conducted at https://www.lc-bio.cn/ (LC Sciences, Hangzhou, China).

Techniques: RNA Sequencing, Isolation

Journal: Frontiers in Neurology

Article Title: Novel Surrogate Markers of CNS Inflammation in CSF in the Diagnosis of Autoimmune Encephalitis

doi: 10.3389/fneur.2019.01390

Figure Lengend Snippet: CSF cytokines. (A) Heat map cluster distinguishes viral from AbPAE and AbNAE encephalitis. Each column represents a participant. The X-axis identifies the cohort each participant belongs to, while the right-handed Y axis describes the corresponding cytokine. Increasing expression is depicted as increasing shades of red. Th1 and proinflammatory cytokines appear to be associated with viral infections, with the addition of IL7a, IL1b, and IL4 associated with enterovirus infections in this group. (B) Cytokines where a significant difference was found in univariate analysis of the autoimmune encephalitis group compared with a combined pool of NI, viral, and other autoimmune disease controls. Cytokines where the statistical significance was also seen in a univariate analysis are indicated with asterisks (* < 0.05, ** < 0.01, *** < 0.001, **** < 0.0001). Statistical significance seen in multivariate analysis are indicated with hatches (# < 0.05, ## < 0.01, ### < 0.001, #### < 0.0001). Lines indicate medians. details the p-values of individual group comparisons. AbPAE, patients clinically high risk for autoimmune encephalitis who had identified associated antibodies; AbNAE, patients clinically high risk for autoimmune encephalitis without identified associated antibodies; NI, samples from patients either undergoing perioperative anesthesia or diagnosed with non-inflammatory neurological diseases; OAND, patients with other inflammatory neurological disease; EBV, Epstein Barr virus; VZV, varicella zoster virus; HSV, herpes simplex virus; ENT, enterovirus.

Article Snippet: Heat map analysis of cytokines was performed using Morpheus (Broad Institute) to find cytokines of potential interest.

Techniques: Expressing, Virus