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heatmap generation heatmap2  (RStudio)

 
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    RStudio heatmap generation heatmap2
    Heatmap Generation Heatmap2, supplied by RStudio, 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/double+gradient+heatmap+plot/heatmap+2+function/pmc06801740-133-7-19
    Average 90 stars, based on 1 article reviews
    heatmap generation heatmap2 - by Bioz Stars, 2026-11
    90/100 stars

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    other:

    Article Title: Fecal bile acid dysmetabolism and reduced ursodeoxycholic acid correlate with novel microbial signatures in feline chronic kidney disease
    Article Snippet: Additional fecal bile acid concentration heatmap generation was performed in R Studio with the heatmap.2 function from the gplots package (v3.1.3) and hierarchical clustering performed with the hclust function.

    Article Title: Understanding emotional and health indicators underlying the burnout risk of healthcare workers.
    Article Snippet: In this study, correlation analysis was performed using Spearman Rank Correlation, with the RStudio stats package’s cor function ("method = spearman"), to obtain the correlation scores, and the gplots package’s heatmap.2 function was used to visualize the relationship between variables based on these scores.

    Article Title: Leiomodin 2 neonatal dilated cardiomyopathy mutation results in altered actin gene signatures and cardiomyocyte dysfunction
    Article Snippet: Differentially expressed genes were calculated using DESeq2, and heatmaps were generated using heatmap.2 plugin in RStudio packages.

    Article Title: Integrated faecal microbiota and blood metabolic changes following different dietary zinc oxide levels in weaned piglets.
    Article Snippet: Pearson’s test with false discovery rate P-value correction was used to determine significance by using the corr.test function and plotted using the heatmap.2 function from the R-package gplots (RStudio, R).

    Article Title: Microbial community variations in adult Hyalomma dromedarii ticks from single locations in Saudi Arabia and Tunisia
    Article Snippet: Later on, the resulting data were used to construct a heatmap using the “ heatmap.2 ” function in RStudio ( ).

    Article Title: Differential Impact of Simultaneous or Sequential Coinfections With Borrelia afzelii and Tick-Borne Encephalitis Virus on the Ixodes ricinus Microbiota
    Article Snippet: The resulting data were used to construct the heatmap with the ‘ heatmap.2 ' function from gplots package [ ] implemented in RStudio environment [ ].

    Software:

    Article Title: Genomic characterization of Leishmania ( V. ) braziliensis associated with antimony therapeutic failure and variable in vitro tolerance to amphotericin B
    Article Snippet: .. A comparative matrix of relative ploidy for the 13 isolates was created, and it was visualized as a Heatmap using the ggplot and heatmap2 packages of R Statistical Software v4.3.0 and RStudio v2023.03.1 . ..

    Article Title: Genomic characterization of Leishmania (V.) braziliensis associated with antimony therapeutic failure and variable in vitro tolerance to amphotericin B.
    Article Snippet: .. A comparative matrix of relative ploidy for the 13 isolates was created, and it was visualized as a Heatmap using the ggplot and heatmap2 packages of R Statistical Software v4.3.0 and RStudio v2023.03.139. ..



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    double gradient heatmap plot  (GraphPad Software Inc)
    90
    GraphPad Software Inc double gradient heatmap plot
    (A) <t>Heatmap</t> of ATARiS gene sensitivity scores of two KRAS dependent cell lines (NCI-H358 and MDA-MB-231) and a BRAF dependent cell line (A375). Negative values (shaded red) indicate sensitivity of the cell line proliferation to the knockdown of shown genes, whereas positive scores (shaded blue) indicate insensitivity. (B) IC 50 values for indicated compounds in Ras pathway mutant cell lines NCI-H358, MDA-MB231 and A375 grown as 3D spheroids under serum free conditions. Compounds were tested either as single agent at a concentration range of 0.2 μM– 10 μM (calmidazolium), 0.6 μM– 40 μM (DT-061), 0.2 μM– 40 μM (trifluoperazine) and 0.6 μM– 40 μM (ARS-1620) or in combination, applying the whole concentration range of calmidazolium combined with 1 μM or 2 μM of DT-061, as indicated. Data represent mean values ± SD, n = 2. Statistical comparisons were done using the average values across all three cell lines. (C) Bliss synergism scores for combinatorial effects of calmidazolium and DT-061 in KRAS- or BRAF-mutant cancer cell lines. Data represent mean values ± SD, n = 2. Positive scores indicate synergistic drug interactions whereas negative scores would denote antagonistic drug interactions. A score of zero would indicate no antagonistic or synergistic effect. ( D ) Flow cytometric analysis of apoptosis in MDA-MB-231 cells. MDA-MB-231 cells were treated with DT-061 (10 μM) or calmidazolium (5 μM) or their combination for 24 h and then labelled with Annexin V-FITC and 7AAD. Benzethonium chloride and DMSO treated cells were used as positive and negative controls, respectively, for setting the gates. Percentage of total apoptotic cells (early and late stage) from two biological repeats (mean ± SD) is presented. Statistical analysis was performed using Fisher’s exact test comparing the total number of viable and apoptotic cells from two biological repeats. ( E ) Effect of inhibitors on cellular apoptosis studied using Caspase-3/7Glo assay. MDA-MB-231 cells were treated with DT-061 (5 μM), calmidazolium (5 μM), combination of DT-061 and calmidazolium (5 μM each), and staurosporine (1 μM) for 24 h. The caspase-3/7 activity was measured as a luminescence read-out and normalized to the vehicle control, 0.05% (v/v) DMSO. Data represent mean values ± SD, n = 2. ( F ) Western blot analysis of PARP-cleavage activity in MDA-MB-231 cells treated with DMSO (0.2% (v/v)), DT-061 (20 μM), calmidazolium (5 μM), combinations of DT-061 (10 μM) and calmidazolium (5 μM), and staurosporine (1 μM) for 24 h. GAPDH detection was used as loading control.
    Double Gradient Heatmap Plot, supplied by GraphPad Software Inc, 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/double+gradient+heatmap+plot/double+gradient+heatmap+plot/pmc09135253-67-21-29
    Average 90 stars, based on 1 article reviews
    double gradient heatmap plot - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier

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    (A) Heatmap of ATARiS gene sensitivity scores of two KRAS dependent cell lines (NCI-H358 and MDA-MB-231) and a BRAF dependent cell line (A375). Negative values (shaded red) indicate sensitivity of the cell line proliferation to the knockdown of shown genes, whereas positive scores (shaded blue) indicate insensitivity. (B) IC 50 values for indicated compounds in Ras pathway mutant cell lines NCI-H358, MDA-MB231 and A375 grown as 3D spheroids under serum free conditions. Compounds were tested either as single agent at a concentration range of 0.2 μM– 10 μM (calmidazolium), 0.6 μM– 40 μM (DT-061), 0.2 μM– 40 μM (trifluoperazine) and 0.6 μM– 40 μM (ARS-1620) or in combination, applying the whole concentration range of calmidazolium combined with 1 μM or 2 μM of DT-061, as indicated. Data represent mean values ± SD, n = 2. Statistical comparisons were done using the average values across all three cell lines. (C) Bliss synergism scores for combinatorial effects of calmidazolium and DT-061 in KRAS- or BRAF-mutant cancer cell lines. Data represent mean values ± SD, n = 2. Positive scores indicate synergistic drug interactions whereas negative scores would denote antagonistic drug interactions. A score of zero would indicate no antagonistic or synergistic effect. ( D ) Flow cytometric analysis of apoptosis in MDA-MB-231 cells. MDA-MB-231 cells were treated with DT-061 (10 μM) or calmidazolium (5 μM) or their combination for 24 h and then labelled with Annexin V-FITC and 7AAD. Benzethonium chloride and DMSO treated cells were used as positive and negative controls, respectively, for setting the gates. Percentage of total apoptotic cells (early and late stage) from two biological repeats (mean ± SD) is presented. Statistical analysis was performed using Fisher’s exact test comparing the total number of viable and apoptotic cells from two biological repeats. ( E ) Effect of inhibitors on cellular apoptosis studied using Caspase-3/7Glo assay. MDA-MB-231 cells were treated with DT-061 (5 μM), calmidazolium (5 μM), combination of DT-061 and calmidazolium (5 μM each), and staurosporine (1 μM) for 24 h. The caspase-3/7 activity was measured as a luminescence read-out and normalized to the vehicle control, 0.05% (v/v) DMSO. Data represent mean values ± SD, n = 2. ( F ) Western blot analysis of PARP-cleavage activity in MDA-MB-231 cells treated with DMSO (0.2% (v/v)), DT-061 (20 μM), calmidazolium (5 μM), combinations of DT-061 (10 μM) and calmidazolium (5 μM), and staurosporine (1 μM) for 24 h. GAPDH detection was used as loading control.

    Journal: PLoS ONE

    Article Title: Potential of phenothiazines to synergistically block calmodulin and reactivate PP2A in cancer cells

    doi: 10.1371/journal.pone.0268635

    Figure Lengend Snippet: (A) Heatmap of ATARiS gene sensitivity scores of two KRAS dependent cell lines (NCI-H358 and MDA-MB-231) and a BRAF dependent cell line (A375). Negative values (shaded red) indicate sensitivity of the cell line proliferation to the knockdown of shown genes, whereas positive scores (shaded blue) indicate insensitivity. (B) IC 50 values for indicated compounds in Ras pathway mutant cell lines NCI-H358, MDA-MB231 and A375 grown as 3D spheroids under serum free conditions. Compounds were tested either as single agent at a concentration range of 0.2 μM– 10 μM (calmidazolium), 0.6 μM– 40 μM (DT-061), 0.2 μM– 40 μM (trifluoperazine) and 0.6 μM– 40 μM (ARS-1620) or in combination, applying the whole concentration range of calmidazolium combined with 1 μM or 2 μM of DT-061, as indicated. Data represent mean values ± SD, n = 2. Statistical comparisons were done using the average values across all three cell lines. (C) Bliss synergism scores for combinatorial effects of calmidazolium and DT-061 in KRAS- or BRAF-mutant cancer cell lines. Data represent mean values ± SD, n = 2. Positive scores indicate synergistic drug interactions whereas negative scores would denote antagonistic drug interactions. A score of zero would indicate no antagonistic or synergistic effect. ( D ) Flow cytometric analysis of apoptosis in MDA-MB-231 cells. MDA-MB-231 cells were treated with DT-061 (10 μM) or calmidazolium (5 μM) or their combination for 24 h and then labelled with Annexin V-FITC and 7AAD. Benzethonium chloride and DMSO treated cells were used as positive and negative controls, respectively, for setting the gates. Percentage of total apoptotic cells (early and late stage) from two biological repeats (mean ± SD) is presented. Statistical analysis was performed using Fisher’s exact test comparing the total number of viable and apoptotic cells from two biological repeats. ( E ) Effect of inhibitors on cellular apoptosis studied using Caspase-3/7Glo assay. MDA-MB-231 cells were treated with DT-061 (5 μM), calmidazolium (5 μM), combination of DT-061 and calmidazolium (5 μM each), and staurosporine (1 μM) for 24 h. The caspase-3/7 activity was measured as a luminescence read-out and normalized to the vehicle control, 0.05% (v/v) DMSO. Data represent mean values ± SD, n = 2. ( F ) Western blot analysis of PARP-cleavage activity in MDA-MB-231 cells treated with DMSO (0.2% (v/v)), DT-061 (20 μM), calmidazolium (5 μM), combinations of DT-061 (10 μM) and calmidazolium (5 μM), and staurosporine (1 μM) for 24 h. GAPDH detection was used as loading control.

    Article Snippet: The normalized viability data for the siRNA knockdown of each gene of interest were downloaded from the project DRIVE and a double gradient heatmap plot was generated using Prism (GraphPad).

    Techniques: Knockdown, Mutagenesis, Concentration Assay, Activity Assay, Control, Western Blot