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: International Journal of Molecular Sciences

Article Title: Regulation of Phenolic Compound Production by Light Varying in Spectral Quality and Total Irradiance

doi: 10.3390/ijms23126533

Figure Lengend Snippet: Heatmaps depicting similarities of PheC profiles among light treatments ( A ) as well as similarities in response of individual PheCs to the same light conditions ( B ). The relative contents of each PheC per treatment were averaged ( n = 5–6) and subsequently normalized to the maximum value among all light treatments. Cluster analysis was performed on normalized PheC quantitative data (distance function: Euclidean distance; linkage function: Average linkage). Specifications of light treatments: W (white), B (blue), R (red), G (green), L (low irradiance 100 µmol m −2 s −1 ), M (medium irradiance 200 µmol m −2 s −1 ), and H (high irradiance 400 µmol m −2 s −1 ). Compounds of interest: FQA (feruloylquinic acid), LUT (lutonarin), SAP (saponarin), ISD (isoscoparin derivative), HSG (homoorientin-7-O-[6-sinp]-glc), HFG (homoorientin-7-O-[6-fer]-glc), ISG (isovitexin-7-O-[6-sinp]-glc), and IFG (isovitexin-7-O-[6-fer]-glc).

Article Snippet: Further cluster analysis and heatmaps illustrating the differences in the relative content of PheCs across treatments differing in spectral compositions and irradiance were created (RStudio, ).

Techniques:

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