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genesifter tm microarray data analysis system  (VizX Labs)

 
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    VizX Labs genesifter tm microarray data analysis system
    Genesifter Tm Microarray Data Analysis System, supplied by VizX Labs, 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/genesifter+microarray+data+analysis+system/genesifter+microarray+data+analysis+system/pmc04307599-67-1-7
    Average 90 stars, based on 1 article reviews
    genesifter tm microarray data analysis system - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Microarray:

    Article Title: Hepatic gene expression profile associated with non-alcoholic steatohepatitis protection by S-nitroso-N-acetylcysteine in ob/ob mice.
    Article Snippet: Hepatic gene expression profile associated with non-alcoholic steatohepatitis protection by S-nitroso-N-acetylcysteine in ob/ob mice q,qq Claudia Pinto Marques Souza de Oliveira*, José Tadeu Stefano, Vicência Mara Rodrigues de Lima, Sandra Valéria de Sá, Fernanda Ibanez Simplicio, Evandro Sobrosa de Mello, Maria Lúcia Corrêa-Giannella, Venâncio Avancini Ferreira Alves, Francisco Rafael Martins Laurindo, Marcelo Ganzarolli de Oliveira, Daniel Giannella-Neto, Flair José Carrilho

    Article Title: Limited redundancy in genes regulated by Cyclin T2 and Cyclin T1
    Article Snippet: .. The microarray data was analyzed using the GeneSifter microarray data analysis system (VizX Labs LLC, Seattle, WA; http://www.genesifter.net ). ..

    Article Title: Identification of molecular pathways affected by pterostilbene, a natural dimethylether analog of resveratrol
    Article Snippet: .. Normalized data from the Affymetrix software were analyzed using the GeneSifter microarray data analysis system (VizX Labs LLC, Seattle, WA; [ ]). ..

    Article Title: Transcriptional Activation of Interferon-Stimulated Genes but Not of Cytokine Genes after Primary Infection of Rhesus Macaques with Dengue Virus Type 1
    Article Snippet: .. Gene expression profiles (txt version of the CHP files) were loaded into the GeneSifter microarray data analysis system (VizX Labs, Seattle, WA). ..

    Article Title: An optimized experimental strategy for efficient conversion of embryonic stem (ES)-derived mouse neural stem (NS) cells into a nearly homogeneous mature neuronal population.
    Article Snippet: Article history: NS cells are a homogeneous Received 2 November 2008 Revised 2 February 2009 Accepted 3 February 2009 Available online 21 February 2009

    Article Title: c-Myb promotes the survival of CD4+CD8+ double positive thymocytes through up-regulation of Bcl-xL
    Article Snippet: Biotin-labeled cRNA from each mouse was individually hybridized to Mouse Genome 430 2.0 (Affymetrix, Santa Clara, CA) Gene Chip for 16 h, and scanned with the Affymetrix Gene-Array Scanner as previously described ( 39 ). c-RNA synthesis, hybridization and data collection were performed at the University of Virginia Gene Chip analysis Core Facility. .. Pairwise analysis of control and mutant sample groups was performed using the GeneSifter microarray data analysis system ( http://www.genesifter.net/ ) (VizX Labs LLC, Seattle, WA) to identify genes with statistically significant (p<0.01 Student’s t-test) >2 fold change in expression within the Gene Ontology group GO:0043067:regulation of programmed cell death ( 40 ). .. Western blotting Electronically sorted DP thymocytes were lysed in (20 mM Tris, 7.4; 100 mM NaCl, 10 mM EDTA; 1 mM EGTA, 1% Triton X-100) ( 41 ) containing EDTA-free protease inhibitor cocktail (Roche, Indianapolis, IN).

    Article Title: Comparison of gene expression profiles in mice liver following intravenous injection of 4 and 100 nm-sized PEG-coated gold nanoparticles.
    Article Snippet: Gold nanoparticles (AuNPs) have been widely used in various biomedical applications for photothermal therapy, imaging and drug delivery.. Although AuNPs have been recognized as a biologically safe material, very little is known about their molecular and cellular effects.. To evaluate the gene expression profile and mechanism of the molecular level of polyethylene glycol (PEG)-coated AuNPs and the effect of particle size, we applied an expression profiling approach.

    Article Title: Characterization of a major colon cancer susceptibility locus (Ccs3) on mouse chromosome 3.
    Article Snippet: Selected RNAs were used for transcriptional profiling with Affymetrix oligonucleotides chips (Mouse Genome 430 2.0 array), according to the manufacturer’s recommendations. .. Raw data generated by GeneChip Operating Software were normalized using GeneSifter microarray data analysis system (VizX Labs, Seattle, WA, USA; www.genesifter.net), using RMA (Robust Multi-Array) normalization. ..

    Generated:

    Article Title: Hepatic gene expression profile associated with non-alcoholic steatohepatitis protection by S-nitroso-N-acetylcysteine in ob/ob mice.
    Article Snippet: Hepatic gene expression profile associated with non-alcoholic steatohepatitis protection by S-nitroso-N-acetylcysteine in ob/ob mice q,qq Claudia Pinto Marques Souza de Oliveira*, José Tadeu Stefano, Vicência Mara Rodrigues de Lima, Sandra Valéria de Sá, Fernanda Ibanez Simplicio, Evandro Sobrosa de Mello, Maria Lúcia Corrêa-Giannella, Venâncio Avancini Ferreira Alves, Francisco Rafael Martins Laurindo, Marcelo Ganzarolli de Oliveira, Daniel Giannella-Neto, Flair José Carrilho

    Article Title: Comparison of gene expression profiles in mice liver following intravenous injection of 4 and 100 nm-sized PEG-coated gold nanoparticles.
    Article Snippet: Gold nanoparticles (AuNPs) have been widely used in various biomedical applications for photothermal therapy, imaging and drug delivery.. Although AuNPs have been recognized as a biologically safe material, very little is known about their molecular and cellular effects.. To evaluate the gene expression profile and mechanism of the molecular level of polyethylene glycol (PEG)-coated AuNPs and the effect of particle size, we applied an expression profiling approach.

    Article Title: Characterization of a major colon cancer susceptibility locus (Ccs3) on mouse chromosome 3.
    Article Snippet: Selected RNAs were used for transcriptional profiling with Affymetrix oligonucleotides chips (Mouse Genome 430 2.0 array), according to the manufacturer’s recommendations. .. Raw data generated by GeneChip Operating Software were normalized using GeneSifter microarray data analysis system (VizX Labs, Seattle, WA, USA; www.genesifter.net), using RMA (Robust Multi-Array) normalization. ..

    Comparison:

    Article Title: Hepatic gene expression profile associated with non-alcoholic steatohepatitis protection by S-nitroso-N-acetylcysteine in ob/ob mice.
    Article Snippet: Hepatic gene expression profile associated with non-alcoholic steatohepatitis protection by S-nitroso-N-acetylcysteine in ob/ob mice q,qq Claudia Pinto Marques Souza de Oliveira*, José Tadeu Stefano, Vicência Mara Rodrigues de Lima, Sandra Valéria de Sá, Fernanda Ibanez Simplicio, Evandro Sobrosa de Mello, Maria Lúcia Corrêa-Giannella, Venâncio Avancini Ferreira Alves, Francisco Rafael Martins Laurindo, Marcelo Ganzarolli de Oliveira, Daniel Giannella-Neto, Flair José Carrilho

    Control:

    Article Title: Hepatic gene expression profile associated with non-alcoholic steatohepatitis protection by S-nitroso-N-acetylcysteine in ob/ob mice.
    Article Snippet: Hepatic gene expression profile associated with non-alcoholic steatohepatitis protection by S-nitroso-N-acetylcysteine in ob/ob mice q,qq Claudia Pinto Marques Souza de Oliveira*, José Tadeu Stefano, Vicência Mara Rodrigues de Lima, Sandra Valéria de Sá, Fernanda Ibanez Simplicio, Evandro Sobrosa de Mello, Maria Lúcia Corrêa-Giannella, Venâncio Avancini Ferreira Alves, Francisco Rafael Martins Laurindo, Marcelo Ganzarolli de Oliveira, Daniel Giannella-Neto, Flair José Carrilho

    Article Title: c-Myb promotes the survival of CD4+CD8+ double positive thymocytes through up-regulation of Bcl-xL
    Article Snippet: Biotin-labeled cRNA from each mouse was individually hybridized to Mouse Genome 430 2.0 (Affymetrix, Santa Clara, CA) Gene Chip for 16 h, and scanned with the Affymetrix Gene-Array Scanner as previously described ( 39 ). c-RNA synthesis, hybridization and data collection were performed at the University of Virginia Gene Chip analysis Core Facility. .. Pairwise analysis of control and mutant sample groups was performed using the GeneSifter microarray data analysis system ( http://www.genesifter.net/ ) (VizX Labs LLC, Seattle, WA) to identify genes with statistically significant (p<0.01 Student’s t-test) >2 fold change in expression within the Gene Ontology group GO:0043067:regulation of programmed cell death ( 40 ). .. Western blotting Electronically sorted DP thymocytes were lysed in (20 mM Tris, 7.4; 100 mM NaCl, 10 mM EDTA; 1 mM EGTA, 1% Triton X-100) ( 41 ) containing EDTA-free protease inhibitor cocktail (Roche, Indianapolis, IN).

    Gene Expression:

    Article Title: Transcriptional Activation of Interferon-Stimulated Genes but Not of Cytokine Genes after Primary Infection of Rhesus Macaques with Dengue Virus Type 1
    Article Snippet: .. Gene expression profiles (txt version of the CHP files) were loaded into the GeneSifter microarray data analysis system (VizX Labs, Seattle, WA). ..

    Mutagenesis:

    Article Title: c-Myb promotes the survival of CD4+CD8+ double positive thymocytes through up-regulation of Bcl-xL
    Article Snippet: Biotin-labeled cRNA from each mouse was individually hybridized to Mouse Genome 430 2.0 (Affymetrix, Santa Clara, CA) Gene Chip for 16 h, and scanned with the Affymetrix Gene-Array Scanner as previously described ( 39 ). c-RNA synthesis, hybridization and data collection were performed at the University of Virginia Gene Chip analysis Core Facility. .. Pairwise analysis of control and mutant sample groups was performed using the GeneSifter microarray data analysis system ( http://www.genesifter.net/ ) (VizX Labs LLC, Seattle, WA) to identify genes with statistically significant (p<0.01 Student’s t-test) >2 fold change in expression within the Gene Ontology group GO:0043067:regulation of programmed cell death ( 40 ). .. Western blotting Electronically sorted DP thymocytes were lysed in (20 mM Tris, 7.4; 100 mM NaCl, 10 mM EDTA; 1 mM EGTA, 1% Triton X-100) ( 41 ) containing EDTA-free protease inhibitor cocktail (Roche, Indianapolis, IN).

    Expressing:

    Article Title: c-Myb promotes the survival of CD4+CD8+ double positive thymocytes through up-regulation of Bcl-xL
    Article Snippet: Biotin-labeled cRNA from each mouse was individually hybridized to Mouse Genome 430 2.0 (Affymetrix, Santa Clara, CA) Gene Chip for 16 h, and scanned with the Affymetrix Gene-Array Scanner as previously described ( 39 ). c-RNA synthesis, hybridization and data collection were performed at the University of Virginia Gene Chip analysis Core Facility. .. Pairwise analysis of control and mutant sample groups was performed using the GeneSifter microarray data analysis system ( http://www.genesifter.net/ ) (VizX Labs LLC, Seattle, WA) to identify genes with statistically significant (p<0.01 Student’s t-test) >2 fold change in expression within the Gene Ontology group GO:0043067:regulation of programmed cell death ( 40 ). .. Western blotting Electronically sorted DP thymocytes were lysed in (20 mM Tris, 7.4; 100 mM NaCl, 10 mM EDTA; 1 mM EGTA, 1% Triton X-100) ( 41 ) containing EDTA-free protease inhibitor cocktail (Roche, Indianapolis, IN).

    Software:

    Article Title: Characterization of a major colon cancer susceptibility locus (Ccs3) on mouse chromosome 3.
    Article Snippet: Selected RNAs were used for transcriptional profiling with Affymetrix oligonucleotides chips (Mouse Genome 430 2.0 array), according to the manufacturer’s recommendations. .. Raw data generated by GeneChip Operating Software were normalized using GeneSifter microarray data analysis system (VizX Labs, Seattle, WA, USA; www.genesifter.net), using RMA (Robust Multi-Array) normalization. ..



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    BMDMs RNA was obtained from individual wt and IRF8 mutant F2 mice either prior to (unstimulated control) or 3 hrs following stimulation with IFNγ/CpG (6 samples per experimental group; 24 samples in total), and hybridized to microarrays. (A) By using a 2×2 interaction Anova analysis, 368 genes were recognized to be significantly differentially modulated by IRF8 in response to IFNγ/CpG exposure between the wt and IRF8 mutant cells. The expression profiles are ordered by hierarchical clustering; the genes, illustrated by their specific signal intensities (Log 2 scale) are displayed as rows and individual mouse samples/conditions as columns. Red coloring signifies high level of expression; green coloring denotes low level of expression. The dendrogram illustrates the clustering of the samples according to expression pattern similarities. RNA samples (6 per experimental group) used for this transcriptional profiling analysis were pooled and used for qPCR validation. Ephx1 , Cyp27a1 , Ciita , and Il10ra were selected as genes positively affected by the presence of functional IRF8 following IFNγ/CpG exposure (B), while Ms4a7 , C1qb , Angptl4 , and Slc40a1 were selected as genes negatively affected by the presence of a functional IRF8 following IFNγ/CpG exposure (C). The ratios of expression (IFNγ/CpG-stimulated versus unstimulated control), represented by fold induction, were calculated for the wt and IRF8 mutant mice separately (white bars), and compared to the corresponding <t>microarray</t> results (black bars). The black dots indicate the qPCR values obtained for each replicate. The microarray results were statistically significant according to Anova analysis ( t test p value of 0.05 and a fold-change cutoff of 1.5X). Hprt was used to standardize the mRNA levels of target genes for qPCR.
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    BMDMs RNA was obtained from individual wt and IRF8 mutant F2 mice either prior to (unstimulated control) or 3 hrs following stimulation with IFNγ/CpG (6 samples per experimental group; 24 samples in total), and hybridized to microarrays. (A) By using a 2×2 interaction Anova analysis, 368 genes were recognized to be significantly differentially modulated by IRF8 in response to IFNγ/CpG exposure between the wt and IRF8 mutant cells. The expression profiles are ordered by hierarchical clustering; the genes, illustrated by their specific signal intensities (Log 2 scale) are displayed as rows and individual mouse samples/conditions as columns. Red coloring signifies high level of expression; green coloring denotes low level of expression. The dendrogram illustrates the clustering of the samples according to expression pattern similarities. RNA samples (6 per experimental group) used for this transcriptional profiling analysis were pooled and used for qPCR validation. Ephx1 , Cyp27a1 , Ciita , and Il10ra were selected as genes positively affected by the presence of functional IRF8 following IFNγ/CpG exposure (B), while Ms4a7 , C1qb , Angptl4 , and Slc40a1 were selected as genes negatively affected by the presence of a functional IRF8 following IFNγ/CpG exposure (C). The ratios of expression (IFNγ/CpG-stimulated versus unstimulated control), represented by fold induction, were calculated for the wt and IRF8 mutant mice separately (white bars), and compared to the corresponding <t>microarray</t> results (black bars). The black dots indicate the qPCR values obtained for each replicate. The microarray results were statistically significant according to Anova analysis ( t test p value of 0.05 and a fold-change cutoff of 1.5X). Hprt was used to standardize the mRNA levels of target genes for qPCR.
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    BMDMs RNA was obtained from individual wt and IRF8 mutant F2 mice either prior to (unstimulated control) or 3 hrs following stimulation with IFNγ/CpG (6 samples per experimental group; 24 samples in total), and hybridized to microarrays. (A) By using a 2×2 interaction Anova analysis, 368 genes were recognized to be significantly differentially modulated by IRF8 in response to IFNγ/CpG exposure between the wt and IRF8 mutant cells. The expression profiles are ordered by hierarchical clustering; the genes, illustrated by their specific signal intensities (Log 2 scale) are displayed as rows and individual mouse samples/conditions as columns. Red coloring signifies high level of expression; green coloring denotes low level of expression. The dendrogram illustrates the clustering of the samples according to expression pattern similarities. RNA samples (6 per experimental group) used for this transcriptional profiling analysis were pooled and used for qPCR validation. Ephx1 , Cyp27a1 , Ciita , and Il10ra were selected as genes positively affected by the presence of functional IRF8 following IFNγ/CpG exposure (B), while Ms4a7 , C1qb , Angptl4 , and Slc40a1 were selected as genes negatively affected by the presence of a functional IRF8 following IFNγ/CpG exposure (C). The ratios of expression (IFNγ/CpG-stimulated versus unstimulated control), represented by fold induction, were calculated for the wt and IRF8 mutant mice separately (white bars), and compared to the corresponding <t>microarray</t> results (black bars). The black dots indicate the qPCR values obtained for each replicate. The microarray results were statistically significant according to Anova analysis ( t test p value of 0.05 and a fold-change cutoff of 1.5X). Hprt was used to standardize the mRNA levels of target genes for qPCR.
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    BMDMs RNA was obtained from individual wt and IRF8 mutant F2 mice either prior to (unstimulated control) or 3 hrs following stimulation with IFNγ/CpG (6 samples per experimental group; 24 samples in total), and hybridized to microarrays. (A) By using a 2×2 interaction Anova analysis, 368 genes were recognized to be significantly differentially modulated by IRF8 in response to IFNγ/CpG exposure between the wt and IRF8 mutant cells. The expression profiles are ordered by hierarchical clustering; the genes, illustrated by their specific signal intensities (Log 2 scale) are displayed as rows and individual mouse samples/conditions as columns. Red coloring signifies high level of expression; green coloring denotes low level of expression. The dendrogram illustrates the clustering of the samples according to expression pattern similarities. RNA samples (6 per experimental group) used for this transcriptional profiling analysis were pooled and used for qPCR validation. Ephx1 , Cyp27a1 , Ciita , and Il10ra were selected as genes positively affected by the presence of functional IRF8 following IFNγ/CpG exposure (B), while Ms4a7 , C1qb , Angptl4 , and Slc40a1 were selected as genes negatively affected by the presence of a functional IRF8 following IFNγ/CpG exposure (C). The ratios of expression (IFNγ/CpG-stimulated versus unstimulated control), represented by fold induction, were calculated for the wt and IRF8 mutant mice separately (white bars), and compared to the corresponding microarray results (black bars). The black dots indicate the qPCR values obtained for each replicate. The microarray results were statistically significant according to Anova analysis ( t test p value of 0.05 and a fold-change cutoff of 1.5X). Hprt was used to standardize the mRNA levels of target genes for qPCR.

    Journal: PLoS Genetics

    Article Title: Interferon Regulatory Factor 8 Regulates Pathways for Antigen Presentation in Myeloid Cells and during Tuberculosis

    doi: 10.1371/journal.pgen.1002097

    Figure Lengend Snippet: BMDMs RNA was obtained from individual wt and IRF8 mutant F2 mice either prior to (unstimulated control) or 3 hrs following stimulation with IFNγ/CpG (6 samples per experimental group; 24 samples in total), and hybridized to microarrays. (A) By using a 2×2 interaction Anova analysis, 368 genes were recognized to be significantly differentially modulated by IRF8 in response to IFNγ/CpG exposure between the wt and IRF8 mutant cells. The expression profiles are ordered by hierarchical clustering; the genes, illustrated by their specific signal intensities (Log 2 scale) are displayed as rows and individual mouse samples/conditions as columns. Red coloring signifies high level of expression; green coloring denotes low level of expression. The dendrogram illustrates the clustering of the samples according to expression pattern similarities. RNA samples (6 per experimental group) used for this transcriptional profiling analysis were pooled and used for qPCR validation. Ephx1 , Cyp27a1 , Ciita , and Il10ra were selected as genes positively affected by the presence of functional IRF8 following IFNγ/CpG exposure (B), while Ms4a7 , C1qb , Angptl4 , and Slc40a1 were selected as genes negatively affected by the presence of a functional IRF8 following IFNγ/CpG exposure (C). The ratios of expression (IFNγ/CpG-stimulated versus unstimulated control), represented by fold induction, were calculated for the wt and IRF8 mutant mice separately (white bars), and compared to the corresponding microarray results (black bars). The black dots indicate the qPCR values obtained for each replicate. The microarray results were statistically significant according to Anova analysis ( t test p value of 0.05 and a fold-change cutoff of 1.5X). Hprt was used to standardize the mRNA levels of target genes for qPCR.

    Article Snippet: The GeneSifter™ microarray data analysis system (Geospiza Inc., Seattle, WA, USA) was used to examine data generated from comparisons between control (unstimulated) and IFNγ/CpG-stimulated (3 hrs) groups.

    Techniques: Mutagenesis, Expressing, Functional Assay, Microarray