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bibliosphere software  (Genomatix gmbh)

 
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    Genomatix gmbh bibliosphere software
    C-MYC and prostate differentiation are targeted by ERG in prostate cancer cells. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the <t>BiblioSphere</t> Software (Genomatix GmbH, Munich, Germany). Red and yellow colors mark upregulation, shades of blue indicate downregulation. For the human tumor gene expression analysis microarray data set was selected from well-differentiated tumors of seven patients with 19-38 folds ERG overexpression (Shaheduzzaman et al., 2007). For assessing gene expression changes in VCaP cells by microarray cells were transfected by ERG si, and were analyzed 48 h post-transfection. The central node of combined ERG si and ERG+ tumor pathways highlights common changes in C-MYC (MYC) and PSA (KLK3) nodes. On the insert (upper left) inhibition of ERG protein expression in VCaP cells in response to various doses of ERG si 48 h post-transfection is shown. (b) MYC expression in response to ERG si inhibition was measured by QRT-PCR and Western blots. Reduced recruitment of ERG to the MYC P2 promoter downstream ETS element was assessed at 48 h post-transfection by ChIP assay by using anti-ERG (ERG) antibody (Ab). IgG and Input was used as controls. (c) PSA mRNA and protein expression were measured by QRT-PCR and Western blot assays respectively. Increased AR binding to the PSA enhancer (ARE) and decreased ERG recruitment to the overlapping ETS cognate element was measured by ChIP assay 48 h after transfection. On the right panel VCaP cells at 9 days after treatment with control NT (upper photographs) and ERG si (lower photographs) were immunostained for CK8/18 (extreme left), PSA (second column from left) and DNA (third column from left) and the separate images merged (extreme right column). The scale bar is 25 micron. (d) SLC45A3 (Prostein) expression in ERG si transfected VCaP cells was measured by Western blots (upper left). Recruitment of AR and ERG to the SLC45A3 promoter upstream ARE and ETS elements was assessed by ChIP assay 48 h post-transfection (lower left). On the table matrix representation of TMPRSS2-ERG expression and SLC45A3 (SLC) immunostaining in prostate tumors of 26 patients (CN=case number) is shown. Sections of whole mounted radical prostatectomy specimens were assessed by immunohistochemistry with anti- SLC45A3 (SLC) antibody. Strong (solid) or weak (grey) staining was correlated with the presence (solid) or absence (hollow) of TMPRSS2-ERG gene fusion transcripts in the same tumors. (e) VCaP cells were transfected with 50 nM of NT or ERG si or MYC si or the combination of 25 nM of ERG si and 25 nM of MYC si. Cell morphology at day 8 is shown. Cell lysates were prepared and assayed by immunoblots with anti-C-MYC or PSA or SLC45A3 (prostein) antibodies. Tubulin was used as the control. ERG-MYC correlation analysis was performed by assessing quantitative gene expression data of C-MYC and ERG or C-MYC and PCA3 from 37 laser capture microdissected human tumors. R and P-values are shown in the table.
    Bibliosphere Software, supplied by Genomatix gmbh, 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/high-density+prostate+tissue+microarray/bibliosphere+software/pmc07556723-63-74-76
    Average 90 stars, based on 1 article reviews
    bibliosphere software - by Bioz Stars, 2026-10
    90/100 stars

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    1) Product Images from "TMPRSS2-ERG Fusion, a Common Genomic Alteration in Prostate Cancer Activates C-MYC and Abrogates Prostate Epithelial Differentiation"

    Article Title: TMPRSS2-ERG Fusion, a Common Genomic Alteration in Prostate Cancer Activates C-MYC and Abrogates Prostate Epithelial Differentiation

    Journal: Oncogene

    doi: 10.1038/onc.2008.183

    C-MYC and prostate differentiation are targeted by ERG in prostate cancer cells. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the BiblioSphere Software (Genomatix GmbH, Munich, Germany). Red and yellow colors mark upregulation, shades of blue indicate downregulation. For the human tumor gene expression analysis microarray data set was selected from well-differentiated tumors of seven patients with 19-38 folds ERG overexpression (Shaheduzzaman et al., 2007). For assessing gene expression changes in VCaP cells by microarray cells were transfected by ERG si, and were analyzed 48 h post-transfection. The central node of combined ERG si and ERG+ tumor pathways highlights common changes in C-MYC (MYC) and PSA (KLK3) nodes. On the insert (upper left) inhibition of ERG protein expression in VCaP cells in response to various doses of ERG si 48 h post-transfection is shown. (b) MYC expression in response to ERG si inhibition was measured by QRT-PCR and Western blots. Reduced recruitment of ERG to the MYC P2 promoter downstream ETS element was assessed at 48 h post-transfection by ChIP assay by using anti-ERG (ERG) antibody (Ab). IgG and Input was used as controls. (c) PSA mRNA and protein expression were measured by QRT-PCR and Western blot assays respectively. Increased AR binding to the PSA enhancer (ARE) and decreased ERG recruitment to the overlapping ETS cognate element was measured by ChIP assay 48 h after transfection. On the right panel VCaP cells at 9 days after treatment with control NT (upper photographs) and ERG si (lower photographs) were immunostained for CK8/18 (extreme left), PSA (second column from left) and DNA (third column from left) and the separate images merged (extreme right column). The scale bar is 25 micron. (d) SLC45A3 (Prostein) expression in ERG si transfected VCaP cells was measured by Western blots (upper left). Recruitment of AR and ERG to the SLC45A3 promoter upstream ARE and ETS elements was assessed by ChIP assay 48 h post-transfection (lower left). On the table matrix representation of TMPRSS2-ERG expression and SLC45A3 (SLC) immunostaining in prostate tumors of 26 patients (CN=case number) is shown. Sections of whole mounted radical prostatectomy specimens were assessed by immunohistochemistry with anti- SLC45A3 (SLC) antibody. Strong (solid) or weak (grey) staining was correlated with the presence (solid) or absence (hollow) of TMPRSS2-ERG gene fusion transcripts in the same tumors. (e) VCaP cells were transfected with 50 nM of NT or ERG si or MYC si or the combination of 25 nM of ERG si and 25 nM of MYC si. Cell morphology at day 8 is shown. Cell lysates were prepared and assayed by immunoblots with anti-C-MYC or PSA or SLC45A3 (prostein) antibodies. Tubulin was used as the control. ERG-MYC correlation analysis was performed by assessing quantitative gene expression data of C-MYC and ERG or C-MYC and PCA3 from 37 laser capture microdissected human tumors. R and P-values are shown in the table.
    Figure Legend Snippet: C-MYC and prostate differentiation are targeted by ERG in prostate cancer cells. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the BiblioSphere Software (Genomatix GmbH, Munich, Germany). Red and yellow colors mark upregulation, shades of blue indicate downregulation. For the human tumor gene expression analysis microarray data set was selected from well-differentiated tumors of seven patients with 19-38 folds ERG overexpression (Shaheduzzaman et al., 2007). For assessing gene expression changes in VCaP cells by microarray cells were transfected by ERG si, and were analyzed 48 h post-transfection. The central node of combined ERG si and ERG+ tumor pathways highlights common changes in C-MYC (MYC) and PSA (KLK3) nodes. On the insert (upper left) inhibition of ERG protein expression in VCaP cells in response to various doses of ERG si 48 h post-transfection is shown. (b) MYC expression in response to ERG si inhibition was measured by QRT-PCR and Western blots. Reduced recruitment of ERG to the MYC P2 promoter downstream ETS element was assessed at 48 h post-transfection by ChIP assay by using anti-ERG (ERG) antibody (Ab). IgG and Input was used as controls. (c) PSA mRNA and protein expression were measured by QRT-PCR and Western blot assays respectively. Increased AR binding to the PSA enhancer (ARE) and decreased ERG recruitment to the overlapping ETS cognate element was measured by ChIP assay 48 h after transfection. On the right panel VCaP cells at 9 days after treatment with control NT (upper photographs) and ERG si (lower photographs) were immunostained for CK8/18 (extreme left), PSA (second column from left) and DNA (third column from left) and the separate images merged (extreme right column). The scale bar is 25 micron. (d) SLC45A3 (Prostein) expression in ERG si transfected VCaP cells was measured by Western blots (upper left). Recruitment of AR and ERG to the SLC45A3 promoter upstream ARE and ETS elements was assessed by ChIP assay 48 h post-transfection (lower left). On the table matrix representation of TMPRSS2-ERG expression and SLC45A3 (SLC) immunostaining in prostate tumors of 26 patients (CN=case number) is shown. Sections of whole mounted radical prostatectomy specimens were assessed by immunohistochemistry with anti- SLC45A3 (SLC) antibody. Strong (solid) or weak (grey) staining was correlated with the presence (solid) or absence (hollow) of TMPRSS2-ERG gene fusion transcripts in the same tumors. (e) VCaP cells were transfected with 50 nM of NT or ERG si or MYC si or the combination of 25 nM of ERG si and 25 nM of MYC si. Cell morphology at day 8 is shown. Cell lysates were prepared and assayed by immunoblots with anti-C-MYC or PSA or SLC45A3 (prostein) antibodies. Tubulin was used as the control. ERG-MYC correlation analysis was performed by assessing quantitative gene expression data of C-MYC and ERG or C-MYC and PCA3 from 37 laser capture microdissected human tumors. R and P-values are shown in the table.

    Techniques Used: Transfection, Quantitative RT-PCR, Chromatin Immunoprecipitation, Western Blot, Functional Assay, Gene Expression, Expressing, Software, Microarray, Over Expression, Inhibition, Binding Assay, Control, Immunostaining, Immunohistochemistry, Staining

    Related Articles

    other:

    Article Title: Gene expression analysis in SV-40 immortalized human corneal epithelial cells cultured with an air-liquid interface
    Article Snippet: Gene networks were inferred using the Genomatix BiblioSphere v. 7.0 software.

    Functional Assay:

    Article Title: Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism
    Article Snippet: .. Apparent functional relationships between genes identified through these analyses were investigated further using DAVID Bioinformatic Resources 6.7 (da Huang et al. 2009a , b ), GO-Elite (Zambon et al. 2012 ) to test for enrichment of pathways included in Wikipathways ( www.wikipathways.org ) using Cytoscape ( www.cytoscape.org ) for visualisation and BiblioSphere literature mining software (Genomatix Software GmbH, Munich, Germany). ..

    Article Title: TMPRSS2-ERG Fusion, a Common Genomic Alteration in Prostate Cancer Activates C-MYC and Abrogates Prostate Epithelial Differentiation
    Article Snippet: .. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the BiblioSphere Software (Genomatix GmbH, Munich, Germany). ..

    Software:

    Article Title: Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism
    Article Snippet: .. Apparent functional relationships between genes identified through these analyses were investigated further using DAVID Bioinformatic Resources 6.7 (da Huang et al. 2009a , b ), GO-Elite (Zambon et al. 2012 ) to test for enrichment of pathways included in Wikipathways ( www.wikipathways.org ) using Cytoscape ( www.cytoscape.org ) for visualisation and BiblioSphere literature mining software (Genomatix Software GmbH, Munich, Germany). ..

    Article Title: Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation
    Article Snippet: .. Regulatory networks which represent gene interactions correlated with transcription profiling were modeled by the Genomatix's Bibliosphere software. pSTIING, which stands for protein, signaling, transcriptional interactions and inflammation networks gateway [ ], was used to describe and to confirm the known interactions and transcriptional associations of these differential genes. ..

    Article Title: Prostate cancer-specific alterations in ERG gene expression and detection and treatment methods based on those alterations
    Article Snippet: .. A two-fold cut-off criterion was applied for further pathway analysis using Bibliosphere Software (Genomatix GmbH, Munich, Germany). ..

    Article Title: Using Polymorphisms in FKBP5 to Define Biologically Distinct Subtypes of Posttraumatic Stress Disorder
    Article Snippet: .. 36 The BiblioSphere data mining software from Genomatix was used for pathway analysis of transcripts. ..

    Article Title: TMPRSS2-ERG Fusion, a Common Genomic Alteration in Prostate Cancer Activates C-MYC and Abrogates Prostate Epithelial Differentiation
    Article Snippet: .. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the BiblioSphere Software (Genomatix GmbH, Munich, Germany). ..

    Transfection:

    Article Title: TMPRSS2-ERG Fusion, a Common Genomic Alteration in Prostate Cancer Activates C-MYC and Abrogates Prostate Epithelial Differentiation
    Article Snippet: .. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the BiblioSphere Software (Genomatix GmbH, Munich, Germany). ..

    Chromatin Immunoprecipitation:

    Article Title: TMPRSS2-ERG Fusion, a Common Genomic Alteration in Prostate Cancer Activates C-MYC and Abrogates Prostate Epithelial Differentiation
    Article Snippet: .. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the BiblioSphere Software (Genomatix GmbH, Munich, Germany). ..

    Western Blot:

    Article Title: TMPRSS2-ERG Fusion, a Common Genomic Alteration in Prostate Cancer Activates C-MYC and Abrogates Prostate Epithelial Differentiation
    Article Snippet: .. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the BiblioSphere Software (Genomatix GmbH, Munich, Germany). ..

    Gene Expression:

    Article Title: TMPRSS2-ERG Fusion, a Common Genomic Alteration in Prostate Cancer Activates C-MYC and Abrogates Prostate Epithelial Differentiation
    Article Snippet: .. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the BiblioSphere Software (Genomatix GmbH, Munich, Germany). ..

    Expressing:

    Article Title: TMPRSS2-ERG Fusion, a Common Genomic Alteration in Prostate Cancer Activates C-MYC and Abrogates Prostate Epithelial Differentiation
    Article Snippet: .. VCaP cells transfected with ERG si or NT were analyzed by Affymetrix HG U133 Plus 2.0 high-density oligonucleotide human genome arrays, QRT-PCR, Chromatin Immunoprecipitation and by Western blots. (a) Functional co-citation based network was obtained from overlapping genes within the comparative gene expression analyses of ERG expressing prostate tumors (ERG+ Tumor Gene Expression, left side color codes) and ERG si treated VCaP cells (ERG si Gene Expression, VCaP, right side color codes) by the BiblioSphere Software (Genomatix GmbH, Munich, Germany). ..



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