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heatmap analysis  (LC Sciences)

 
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    LC Sciences heatmap analysis
    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 <t>KEGG</t> 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. <t>D</t> <t>Heatmap</t> 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.
    Heatmap Analysis, supplied by LC Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/heatmap+analysis/heatmap+analysis/pmc08511105-57-11-23
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    Images

    1) Product Images from "Downregulation of phosphoglycerate mutase 5 improves microglial inflammasome activation after traumatic brain injury"

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

    Journal: Cell Death Discovery

    doi: 10.1038/s41420-021-00686-8

    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.
    Figure Legend 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.

    Techniques Used: RNA Sequencing, Isolation

    Related Articles

    RNA Sequencing:

    Article Title: Downregulation of phosphoglycerate mutase 5 improves microglial inflammasome activation after traumatic brain injury
    Article Snippet: of significant difference was |log2foldchange | ≥1, p < 0.05. .. 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).

    Isolation:

    Article Title: Downregulation of phosphoglycerate mutase 5 improves microglial inflammasome activation after traumatic brain injury
    Article Snippet: of significant difference was |log2foldchange | ≥1, p < 0.05. .. 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).



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    Image Search Results


    Characterization of cHep. A. Direct differentiation of cryopreserved pre-cHep using a protocol equivalent to 3D PHH spheroid formation. B. Representative images of 3D PHH and cHep. C. Principal component analysis (PCA) plot including cHep generated from day 30 (D30) J03, J06, and J13 L4 pre-cHep, 3D PHH, and published hepatocyte-like cells (HLC). D. Heatmap showing expression of 264 liver-enriched genes. E–H. Distance-based similarity scores based on gene expression associated with xenobiotic metabolism (E), amino acid biosynthesis (F), bile acid biosynthesis (G), and the urea cycle (H). I. Immunofluorescence staining for albumin, HNF4α, CYP2E1, and ASGR1. J. Cholyl-lysyl-fluorescein (CLF) staining.

    Journal: bioRxiv

    Article Title: Precursor of chemically expanded hepatocytes (pre-cHep) with 1-million-fold expansion potential and liver repopulation capacity

    doi: 10.64898/2026.05.15.725446

    Figure Lengend Snippet: Characterization of cHep. A. Direct differentiation of cryopreserved pre-cHep using a protocol equivalent to 3D PHH spheroid formation. B. Representative images of 3D PHH and cHep. C. Principal component analysis (PCA) plot including cHep generated from day 30 (D30) J03, J06, and J13 L4 pre-cHep, 3D PHH, and published hepatocyte-like cells (HLC). D. Heatmap showing expression of 264 liver-enriched genes. E–H. Distance-based similarity scores based on gene expression associated with xenobiotic metabolism (E), amino acid biosynthesis (F), bile acid biosynthesis (G), and the urea cycle (H). I. Immunofluorescence staining for albumin, HNF4α, CYP2E1, and ASGR1. J. Cholyl-lysyl-fluorescein (CLF) staining.

    Article Snippet: Hierarchical clustering and gene expression heatmap analysis of 264 liver-enriched genes from Human Protein Atlas (gene list in Supplementary Table S3) also showed that D30 cHep clustered closely with 3D PHH, although expression of some genes remained lower than in uncultured PHH and liver samples ( ).

    Techniques: Generated, Expressing, Gene Expression, Immunofluorescence, Staining

    Gene expression analysis of HLC. Distance-based similarity score and gene expression heatmap with KEGG gene sets: Fatty acid metabolism (A, D), Retinol metabolism (B, E) and Complement coagulation cascade (C, F).

    Journal: bioRxiv

    Article Title: Precursor of chemically expanded hepatocytes (pre-cHep) with 1-million-fold expansion potential and liver repopulation capacity

    doi: 10.64898/2026.05.15.725446

    Figure Lengend Snippet: Gene expression analysis of HLC. Distance-based similarity score and gene expression heatmap with KEGG gene sets: Fatty acid metabolism (A, D), Retinol metabolism (B, E) and Complement coagulation cascade (C, F).

    Article Snippet: Hierarchical clustering and gene expression heatmap analysis of 264 liver-enriched genes from Human Protein Atlas (gene list in Supplementary Table S3) also showed that D30 cHep clustered closely with 3D PHH, although expression of some genes remained lower than in uncultured PHH and liver samples ( ).

    Techniques: Gene Expression, Coagulation

    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.

    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