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dna microarray gene expression datasets  (Biotechnology Information)

 
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    Biotechnology Information dna microarray gene expression datasets
    Workflow of this study. The <t>DNA</t> <t>microarray</t> gene expression datasets of 92 borderline ovarian tumor (BOT) samples and 136 normal ovarian controls were downloaded from a publicly available database with the gene set regularity (GSR) index calculated by the Gene Ontology (GO) gene set. Functionomes consisting of 10,192 GO gene sets established from the polygenic model and machine learning with statistical methods and cumulative portion transformations were used to recognize the functionome patterns to discover dysfunctional GO terms, pathways, and differentially expressed genes (DEGs). Finally, the pathogenesis of BOTs was investigated by integrative analysis.
    Dna Microarray Gene Expression Datasets, supplied by Biotechnology Information, 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/dna+microarray+gene+expression+datasets/dna+microarray/pmc08071470-183-0-12
    Average 90 stars, based on 1 article reviews
    dna microarray gene expression datasets - by Bioz Stars, 2026-09
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    1) Product Images from "Dysregulated Immunological Functionome and Dysfunctional Metabolic Pathway Recognized for the Pathogenesis of Borderline Ovarian Tumors by Integrative Polygenic Analytics"

    Article Title: Dysregulated Immunological Functionome and Dysfunctional Metabolic Pathway Recognized for the Pathogenesis of Borderline Ovarian Tumors by Integrative Polygenic Analytics

    Journal: International Journal of Molecular Sciences

    doi: 10.3390/ijms22084105

    Workflow of this study. The DNA microarray gene expression datasets of 92 borderline ovarian tumor (BOT) samples and 136 normal ovarian controls were downloaded from a publicly available database with the gene set regularity (GSR) index calculated by the Gene Ontology (GO) gene set. Functionomes consisting of 10,192 GO gene sets established from the polygenic model and machine learning with statistical methods and cumulative portion transformations were used to recognize the functionome patterns to discover dysfunctional GO terms, pathways, and differentially expressed genes (DEGs). Finally, the pathogenesis of BOTs was investigated by integrative analysis.
    Figure Legend Snippet: Workflow of this study. The DNA microarray gene expression datasets of 92 borderline ovarian tumor (BOT) samples and 136 normal ovarian controls were downloaded from a publicly available database with the gene set regularity (GSR) index calculated by the Gene Ontology (GO) gene set. Functionomes consisting of 10,192 GO gene sets established from the polygenic model and machine learning with statistical methods and cumulative portion transformations were used to recognize the functionome patterns to discover dysfunctional GO terms, pathways, and differentially expressed genes (DEGs). Finally, the pathogenesis of BOTs was investigated by integrative analysis.

    Techniques Used: Microarray, Gene Expression

    Related Articles

    Microarray:

    Article Title: Gene set-based analysis of mucinous ovarian carcinoma.
    Article Snippet: .. Sample information and means of the GSR indexes of MOC DNA microarray gene expression datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database, including 45 MOC and 45 normal ovarian tissue control samples. ..

    Article Title: The notch target gene HEYL modulates metastasis forming capacity of colorectal cancer patient-derived spheroid cells in vivo
    Article Snippet: Numbers of patients with AJCC stage IV colorectal cancer in contrast to AJCC stage I-III colorectal cancer were analyzed using the chi-squared test. .. Whole human genome expression DNA microarray data sets of patients with CRC were obtained via National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) [ ]. .. All expression levels were measured as signal intensity within the Affymetrix Human Genome U133 Plus 2.0 Array.

    Article Title: Expression of S100A8 protein on B cells is associated with disease activity in patients with systemic lupus erythematosus.
    Article Snippet: .. Availability of data and materials The datasets of DNA microarray generated during this study are available in National Center for Biotechnology Information (GSE: 148,601). .. The datasets of LC-MSMS generated during this study are not publicly available due to an intellectual property protection agreement with Astellas Pharma Inc.

    Article Title: The Potential Role of Complement System in the Progression of Ovarian Clear Cell Carcinoma Inferred from the Gene Ontology-Based Immunofunctionome Analysis
    Article Snippet: .. DNA microarray gene expression datasets were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, including 23 samples of stage I, 4 samples of stage II, 12 samples of stage III, 5 samples of stage IV, and 41 samples of unconfirmed stages. ..

    Article Title: Dysregulated Immunological Functionome and Dysfunctional Metabolic Pathway Recognized for the Pathogenesis of Borderline Ovarian Tumors by Integrative Polygenic Analytics
    Article Snippet: .. DNA microarray gene expression datasets were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, and the sample data were obtained from 28 dataset series containing six different DNA microarray platforms without any missing data. ..

    Article Title: Synergistic AHR Binding Pathway with EMT Effects on Serous Ovarian Tumors Recognized by Multidisciplinary Integrated Analysis
    Article Snippet: .. The gene expression profiles of DNA microarray of serous ovarian tumors and normal controls were downloaded from the GEO repository at the National Center for Biotechnology Information (NCBI) archives. ..

    Article Title: Expression of S100A8 protein on B cells is associated with disease activity in patients with systemic lupus erythematosus
    Article Snippet: .. The datasets of DNA microarray generated during this study are available in National Center for Biotechnology Information (GSE: 148,601). .. The datasets of LC-MSMS generated during this study are not publicly available due to an intellectual property protection agreement with Astellas Pharma Inc.

    Gene Expression:

    Article Title: Gene set-based analysis of mucinous ovarian carcinoma.
    Article Snippet: .. Sample information and means of the GSR indexes of MOC DNA microarray gene expression datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database, including 45 MOC and 45 normal ovarian tissue control samples. ..

    Article Title: The notch target gene HEYL modulates metastasis forming capacity of colorectal cancer patient-derived spheroid cells in vivo
    Article Snippet: Numbers of patients with AJCC stage IV colorectal cancer in contrast to AJCC stage I-III colorectal cancer were analyzed using the chi-squared test. .. Whole human genome expression DNA microarray data sets of patients with CRC were obtained via National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) [ ]. .. All expression levels were measured as signal intensity within the Affymetrix Human Genome U133 Plus 2.0 Array.

    Article Title: The CINSARC signature predicts the clinical outcome in patients with Luminal B breast cancer
    Article Snippet: .. Gene expression profiles had been generated using DNA microarrays and RNA-Seq, and collected from the National Center for Biotechnology Information (NCBI)/Genbank GEO and ArrayExpress databases, and authors’ website. ..

    Article Title: The Potential Role of Complement System in the Progression of Ovarian Clear Cell Carcinoma Inferred from the Gene Ontology-Based Immunofunctionome Analysis
    Article Snippet: .. DNA microarray gene expression datasets were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, including 23 samples of stage I, 4 samples of stage II, 12 samples of stage III, 5 samples of stage IV, and 41 samples of unconfirmed stages. ..

    Article Title: Dysregulated Immunological Functionome and Dysfunctional Metabolic Pathway Recognized for the Pathogenesis of Borderline Ovarian Tumors by Integrative Polygenic Analytics
    Article Snippet: .. DNA microarray gene expression datasets were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, and the sample data were obtained from 28 dataset series containing six different DNA microarray platforms without any missing data. ..

    Article Title: Synergistic AHR Binding Pathway with EMT Effects on Serous Ovarian Tumors Recognized by Multidisciplinary Integrated Analysis
    Article Snippet: .. The gene expression profiles of DNA microarray of serous ovarian tumors and normal controls were downloaded from the GEO repository at the National Center for Biotechnology Information (NCBI) archives. ..

    Control:

    Article Title: Gene set-based analysis of mucinous ovarian carcinoma.
    Article Snippet: .. Sample information and means of the GSR indexes of MOC DNA microarray gene expression datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database, including 45 MOC and 45 normal ovarian tissue control samples. ..

    Expressing:

    Article Title: The notch target gene HEYL modulates metastasis forming capacity of colorectal cancer patient-derived spheroid cells in vivo
    Article Snippet: Numbers of patients with AJCC stage IV colorectal cancer in contrast to AJCC stage I-III colorectal cancer were analyzed using the chi-squared test. .. Whole human genome expression DNA microarray data sets of patients with CRC were obtained via National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) [ ]. .. All expression levels were measured as signal intensity within the Affymetrix Human Genome U133 Plus 2.0 Array.

    Generated:

    Article Title: Expression of S100A8 protein on B cells is associated with disease activity in patients with systemic lupus erythematosus.
    Article Snippet: .. Availability of data and materials The datasets of DNA microarray generated during this study are available in National Center for Biotechnology Information (GSE: 148,601). .. The datasets of LC-MSMS generated during this study are not publicly available due to an intellectual property protection agreement with Astellas Pharma Inc.

    Article Title: The CINSARC signature predicts the clinical outcome in patients with Luminal B breast cancer
    Article Snippet: .. Gene expression profiles had been generated using DNA microarrays and RNA-Seq, and collected from the National Center for Biotechnology Information (NCBI)/Genbank GEO and ArrayExpress databases, and authors’ website. ..

    Article Title: Expression of S100A8 protein on B cells is associated with disease activity in patients with systemic lupus erythematosus
    Article Snippet: .. The datasets of DNA microarray generated during this study are available in National Center for Biotechnology Information (GSE: 148,601). .. The datasets of LC-MSMS generated during this study are not publicly available due to an intellectual property protection agreement with Astellas Pharma Inc.



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    Workflow of this study. The <t>DNA</t> <t>microarray</t> gene expression datasets of 92 borderline ovarian tumor (BOT) samples and 136 normal ovarian controls were downloaded from a publicly available database with the gene set regularity (GSR) index calculated by the Gene Ontology (GO) gene set. Functionomes consisting of 10,192 GO gene sets established from the polygenic model and machine learning with statistical methods and cumulative portion transformations were used to recognize the functionome patterns to discover dysfunctional GO terms, pathways, and differentially expressed genes (DEGs). Finally, the pathogenesis of BOTs was investigated by integrative analysis.
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    Workflow of this study. The <t>DNA</t> <t>microarray</t> gene expression datasets of 92 borderline ovarian tumor (BOT) samples and 136 normal ovarian controls were downloaded from a publicly available database with the gene set regularity (GSR) index calculated by the Gene Ontology (GO) gene set. Functionomes consisting of 10,192 GO gene sets established from the polygenic model and machine learning with statistical methods and cumulative portion transformations were used to recognize the functionome patterns to discover dysfunctional GO terms, pathways, and differentially expressed genes (DEGs). Finally, the pathogenesis of BOTs was investigated by integrative analysis.
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    A: Supervised hierarchical clustering displaying the genes significantly modulated between the resistant and sensitive cell lines (52 under‐ and 51 over‐expressed in resistant cell lines) using a cutoff of twofold change on expression and FDR < 0.01. B: Fold difference in gene expression between sensitive and resistant cell lines detected by qRT‐PCR analyses. Seven genes were selected from the list of altered genes for this analysis. The results from sensitive or resistant cell lines were pooled to obtain an estimated fold change. C: Correlation between the qRT‐PCR and the <t>microarray</t> expression data. The fold difference detected by qRT‐PCR between sensitive and resistant cell lines correlated significantly confirming the microarray results (Pearson's correlation or ρ = 0.739, p ‐value = 0.013).
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    Image Search Results


    Workflow of this study. The DNA microarray gene expression datasets of 92 borderline ovarian tumor (BOT) samples and 136 normal ovarian controls were downloaded from a publicly available database with the gene set regularity (GSR) index calculated by the Gene Ontology (GO) gene set. Functionomes consisting of 10,192 GO gene sets established from the polygenic model and machine learning with statistical methods and cumulative portion transformations were used to recognize the functionome patterns to discover dysfunctional GO terms, pathways, and differentially expressed genes (DEGs). Finally, the pathogenesis of BOTs was investigated by integrative analysis.

    Journal: International Journal of Molecular Sciences

    Article Title: Dysregulated Immunological Functionome and Dysfunctional Metabolic Pathway Recognized for the Pathogenesis of Borderline Ovarian Tumors by Integrative Polygenic Analytics

    doi: 10.3390/ijms22084105

    Figure Lengend Snippet: Workflow of this study. The DNA microarray gene expression datasets of 92 borderline ovarian tumor (BOT) samples and 136 normal ovarian controls were downloaded from a publicly available database with the gene set regularity (GSR) index calculated by the Gene Ontology (GO) gene set. Functionomes consisting of 10,192 GO gene sets established from the polygenic model and machine learning with statistical methods and cumulative portion transformations were used to recognize the functionome patterns to discover dysfunctional GO terms, pathways, and differentially expressed genes (DEGs). Finally, the pathogenesis of BOTs was investigated by integrative analysis.

    Article Snippet: DNA microarray gene expression datasets were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, and the sample data were obtained from 28 dataset series containing six different DNA microarray platforms without any missing data.

    Techniques: Microarray, Gene Expression

    A: Supervised hierarchical clustering displaying the genes significantly modulated between the resistant and sensitive cell lines (52 under‐ and 51 over‐expressed in resistant cell lines) using a cutoff of twofold change on expression and FDR < 0.01. B: Fold difference in gene expression between sensitive and resistant cell lines detected by qRT‐PCR analyses. Seven genes were selected from the list of altered genes for this analysis. The results from sensitive or resistant cell lines were pooled to obtain an estimated fold change. C: Correlation between the qRT‐PCR and the microarray expression data. The fold difference detected by qRT‐PCR between sensitive and resistant cell lines correlated significantly confirming the microarray results (Pearson's correlation or ρ = 0.739, p ‐value = 0.013).

    Journal: The Journal of Pathology: Clinical Research

    Article Title: A 12‐gene signature to distinguish colon cancer patients with better clinical outcome following treatment with 5‐fluorouracil or FOLFIRI

    doi: 10.1002/cjp2.17

    Figure Lengend Snippet: A: Supervised hierarchical clustering displaying the genes significantly modulated between the resistant and sensitive cell lines (52 under‐ and 51 over‐expressed in resistant cell lines) using a cutoff of twofold change on expression and FDR < 0.01. B: Fold difference in gene expression between sensitive and resistant cell lines detected by qRT‐PCR analyses. Seven genes were selected from the list of altered genes for this analysis. The results from sensitive or resistant cell lines were pooled to obtain an estimated fold change. C: Correlation between the qRT‐PCR and the microarray expression data. The fold difference detected by qRT‐PCR between sensitive and resistant cell lines correlated significantly confirming the microarray results (Pearson's correlation or ρ = 0.739, p ‐value = 0.013).

    Article Snippet: Hence, we used a publically available gene expression DNA microarray dataset generated by Almac Diagnostics on 359 FFPE tissue specimens from stage II colon cancer that did not receive adjuvant chemotherapy.

    Techniques: Expressing, Gene Expression, Quantitative RT-PCR, Microarray