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heat map generated with cluster 3.0 and java treeview software  (SourceForge net)

 
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    SourceForge net heat map generated with cluster 3.0 and java treeview software
    Heat Map Generated With Cluster 3.0 And Java Treeview Software, supplied by SourceForge net, 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/cluster+treeview/heat+map+generated+with+cluster+3+0+and+java+treeview+software/pmc12187458-114-11-18
    Average 90 stars, based on 1 article reviews
    heat map generated with cluster 3.0 and java treeview software - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    other:

    Article Title: A Natural Light/Dark Cycle Regulation of Carbon-Nitrogen Metabolism and Gene Expression in Rice Shoots
    Article Snippet: The differentially expressed genes and miRNAs were clustered by Cluster 3.0 /TreeView ( http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm , http://jtreeview.sourceforge.net ).

    Article Title: Genetic Interaction Between Lyn, Ets1, and Btk in the Control of Antibody Levels
    Article Snippet: The hierarchical clustering analysis of autoAbs was performed using Cluster and Treeview software (originally obtained from http://rana.lbl.gov/EisenSoftware.htm , currently available at http://bonsai.hgc.jp/~mdehoon/software/cluster/ and http://sourceforge.net/projects/jtreeview/files/jtreeview/ )

    Article Title: Influence of gene modification in biological behaviors and responses of mouse lung telocytes to inflammation
    Article Snippet: The differentially expressed mRNA and lncRNAs were used for a hierarchical clustering analysis (HCA) in Cluster and TreeView ( https://sourceforge.net/projects/jtreeview/files/ ).

    Article Title: UVB Induces a Genome-Wide Acting Negative Regulatory Mechanism That Operates at the Level of Transcription Initiation in Human Cells
    Article Snippet: Cluster: http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/index.html#Top Treeview: http://sourceforge.net/projects/jtreeview/

    Article Title: Analysis of long non-coding RNA expression profiles in ovarian cancer
    Article Snippet: To visually inspect the result of a ‘leave one dataset out’ cross-validation, the differentially expressed lncRNAs of GSE36668 and GSE18520 were used for a hierarchical clustering analysis (HCA) in Cluster and TreeView ( https://sourceforge.net/projects/jtreeview/files/ ) ( ) and ‘gplots’ packages in R. Principal component analysis (PCA) was also performed using TM4 ( ) and R 3.1.4 using the princomp function; the ‘plot3d’ package in R was used to draw a three-dimensional plot.

    Article Title: CAMK2D: a novel molecular target for BAP1 -deficient malignant mesothelioma
    Article Snippet: The heatmap was constructed based on the normalized values of all samples using TreeView (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ).

    Article Title: High Throughput Chemical Screening Reveals Multiple Regulatory Proteins on FOXA1 in Breast Cancer Cell Lines
    Article Snippet: Heat map of the second screening was generated with Java TreeView Cluster 3.0 ( https://sourceforge.net/projects/jtreeview/ ).

    Software:

    Article Title: ZO-1 and IL-1RAP Phosphorylation: Potential Role in Mediated Brain-Gut Axis Dysregulation in Irritable Bowel Syndrome-like Stressed Mice.
    Article Snippet: Phosphorylated protein quantification and identification: We utilize the MASCOT engine (Matrix Science, London, UK; version 2.2) to analyze MS/MS spectra integrated within Proteome Discoverer 2.4. .. Phosphorylated peptide cluster evaluation: The hierarchical clustering process employed Java Treeview software (http://jtreeview.sourceforge.net) alongside Cluster 3.0. ..



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    Heat Map Generated With Cluster 3.0 And Java Treeview Software, supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
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    a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
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    a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
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    a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
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    a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
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    a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
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    Gene expression studies investigating the pathogenesis of RA
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    Image Search Results


    a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using TreeView (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.

    Journal: Cell Death Discovery

    Article Title: CAMK2D: a novel molecular target for BAP1 -deficient malignant mesothelioma

    doi: 10.1038/s41420-023-01552-5

    Figure Lengend Snippet: a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using TreeView (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.

    Article Snippet: The heatmap was constructed based on the normalized values of all samples using TreeView (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ).

    Techniques: CRISPR, Sequencing, Clone Assay, Expressing, Western Blot, Control, Gene Expression, Construct, Reverse Transcription Polymerase Chain Reaction

    Gene expression studies investigating the pathogenesis of RA

    Journal: The Pharmacogenomics Journal

    Article Title: Gene expression analysis in RA: towards personalized medicine

    doi: 10.1038/tpj.2013.48

    Figure Lengend Snippet: Gene expression studies investigating the pathogenesis of RA

    Article Snippet: , Whole blood , Discovery set 14 RA, validation set 26 RA , Illumina , SAM, hierarchial clustering (treeview), Ingenuity pathway analysis , Responders vs non-responders , Significant differential expression of IFN-type I response genes (IRGs) at 6 months of RTX treatment. Baseline prediction of non-response to RTX with a 3 and 8 IFN type I response gene signature , Raterman et al. .

    Techniques: Gene Expression, Comparison, Expressing, Software, Clone Assay, Diagnostic Assay, Activity Assay, Biomarker Discovery

    Gene expression signatures as a tool for treatment outcome prediction

    Journal: The Pharmacogenomics Journal

    Article Title: Gene expression analysis in RA: towards personalized medicine

    doi: 10.1038/tpj.2013.48

    Figure Lengend Snippet: Gene expression signatures as a tool for treatment outcome prediction

    Article Snippet: , Whole blood , Discovery set 14 RA, validation set 26 RA , Illumina , SAM, hierarchial clustering (treeview), Ingenuity pathway analysis , Responders vs non-responders , Significant differential expression of IFN-type I response genes (IRGs) at 6 months of RTX treatment. Baseline prediction of non-response to RTX with a 3 and 8 IFN type I response gene signature , Raterman et al. .

    Techniques: Gene Expression, Software, Comparison, Expressing, Microarray, Biomarker Discovery, Activation Assay, Real-time Polymerase Chain Reaction, Quantitative Proteomics