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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
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heat map generated with cluster 3.0 and java treeview software - by Bioz Stars, 2026-06
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treeview (cluster 3.0)  (SourceForge net)
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SourceForge net treeview (cluster 3.0)
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.
Treeview (Cluster 3.0), 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/result/treeview (cluster 3.0)/product/SourceForge net
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treeview (cluster 3.0) - by Bioz Stars, 2026-06
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cluster treeview software  (Partek)
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Partek cluster treeview software
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.
Cluster Treeview Software, supplied by Partek, 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/result/cluster treeview software/product/Partek
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cluster treeview software - by Bioz Stars, 2026-06
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cluster/treeview files  (Mendeley Ltd)
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Mendeley Ltd cluster/treeview files
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.
Cluster/Treeview Files, supplied by Mendeley Ltd, 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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cluster/treeview files - by Bioz Stars, 2026-06
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cluster and treeview  (SourceForge net)
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SourceForge net cluster and treeview
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.
Cluster And Treeview, 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/result/cluster and treeview/product/SourceForge net
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cluster and treeview - by Bioz Stars, 2026-06
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java treeview cluster 3.0  (SourceForge net)
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SourceForge net java treeview cluster 3.0
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.
Java Treeview Cluster 3.0, 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/result/java treeview cluster 3.0/product/SourceForge net
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java treeview cluster 3.0 - by Bioz Stars, 2026-06
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cluster 3.0 /treeview  (SourceForge net)
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SourceForge net cluster 3.0 /treeview
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.
Cluster 3.0 /Treeview, 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/result/cluster 3.0 /treeview/product/SourceForge net
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cluster 3.0 /treeview - by Bioz Stars, 2026-06
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sam, hierarchical clustering (treeview)  (Illumina Inc)
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Illumina Inc sam, hierarchical clustering (treeview)
Gene expression studies investigating the pathogenesis of RA
Sam, Hierarchical Clustering (Treeview), supplied by Illumina Inc, 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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sam, hierarchical clustering (treeview) - by Bioz Stars, 2026-06
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cluster treeview  (corel corporation)
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corel corporation cluster treeview
Gene expression studies investigating the pathogenesis of RA
Cluster Treeview, supplied by corel corporation, 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/result/cluster treeview/product/corel corporation
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cluster treeview - by Bioz Stars, 2026-06
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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 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