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gep microarray analysis  (Illumina Inc)


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    Illumina Inc gep microarray analysis
    Distinct <t>gene</t> <t>expression</t> <t>profile</t> and enrichment of stem cells signature identified in diagnostic MNCs from patients who failed to achieve EMR. (A) The workflow of our study with regard to the discovery process, including samples from patients with EMR failure (n = 13) vs EMR achievement (n = 83), as defined by BCR-ABL1 percentage at 3 months. (B) Volcano plot demonstrating the effect of log2 fold change (FC) on the x-axis vs −log10 P value on the y-axis. Red circles indicate significant genes (FDR P < .05 and log2 FC > 0.6) with increased gene expression in the EMR failure patient group. Green circles indicate significant genes (FDR P < .05 and log2 FC < −0.6) with decreased gene expression in the EMR failure patient group. (C) Heatmap demonstrating the distinct gene expression patterns based on all significant probes (n = 502; FDR P < .05 and log2 FC > |0.6|). Orange represents increased gene expression level, and blue represents decreased gene expression level. The heatmap was generated using the pheatmap package. (D) GSEA indicates enrichment of stem cell signaling, cell cycle, and immune response/T lymphocytes in the EMR failure patient samples (BCR-ABL1 >10% IS at 3 months) compared with the EMR achievement patient samples (BCR-ABL1 ≤10% IS at 3 months). Blue bars represent cell cycle–related data sets. Red bars represent stem cell–related data sets. Green bars represent immune response/T lymphocyte–related signatures. Regarding normalized enrichment score (NES), positive score indicates positive enrichment in samples from patients who failed to achieve EMR, and negative score indicates enrichment in samples from patients who achieved EMR. (E) Boxplot displaying the differential blast percentage counts at diagnosis, indicating a significantly higher percentage in the samples collected from patients who failed to achieve EMR. Only 91 patients had differential blast percentage counts at diagnosis information available for analysis. (F) Boxplot displaying the lymphocyte percentage counts at diagnosis, indicating a significantly lower percentage in the EMR failure patient sample group. Only 94 patients had lymphocyte percentage counts at diagnosis information available for analysis. Statistical analysis was performed using the Mann-Whitney U test.
    Gep Microarray Analysis, 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
    https://www.bioz.com/product/gep+microarray+analysis/gep+microarray+analysis/pmc06538873-78-3-12
    Average 90 stars, based on 1 article reviews
    gep microarray analysis - by Bioz Stars, 2026-09
    90/100 stars

    Images

    1) Product Images from "Gene expression signature that predicts early molecular response failure in chronic-phase CML patients on frontline imatinib"

    Article Title: Gene expression signature that predicts early molecular response failure in chronic-phase CML patients on frontline imatinib

    Journal: Blood Advances

    doi: 10.1182/bloodadvances.2019000195

    Distinct gene expression profile and enrichment of stem cells signature identified in diagnostic MNCs from patients who failed to achieve EMR. (A) The workflow of our study with regard to the discovery process, including samples from patients with EMR failure (n = 13) vs EMR achievement (n = 83), as defined by BCR-ABL1 percentage at 3 months. (B) Volcano plot demonstrating the effect of log2 fold change (FC) on the x-axis vs −log10 P value on the y-axis. Red circles indicate significant genes (FDR P < .05 and log2 FC > 0.6) with increased gene expression in the EMR failure patient group. Green circles indicate significant genes (FDR P < .05 and log2 FC < −0.6) with decreased gene expression in the EMR failure patient group. (C) Heatmap demonstrating the distinct gene expression patterns based on all significant probes (n = 502; FDR P < .05 and log2 FC > |0.6|). Orange represents increased gene expression level, and blue represents decreased gene expression level. The heatmap was generated using the pheatmap package. (D) GSEA indicates enrichment of stem cell signaling, cell cycle, and immune response/T lymphocytes in the EMR failure patient samples (BCR-ABL1 >10% IS at 3 months) compared with the EMR achievement patient samples (BCR-ABL1 ≤10% IS at 3 months). Blue bars represent cell cycle–related data sets. Red bars represent stem cell–related data sets. Green bars represent immune response/T lymphocyte–related signatures. Regarding normalized enrichment score (NES), positive score indicates positive enrichment in samples from patients who failed to achieve EMR, and negative score indicates enrichment in samples from patients who achieved EMR. (E) Boxplot displaying the differential blast percentage counts at diagnosis, indicating a significantly higher percentage in the samples collected from patients who failed to achieve EMR. Only 91 patients had differential blast percentage counts at diagnosis information available for analysis. (F) Boxplot displaying the lymphocyte percentage counts at diagnosis, indicating a significantly lower percentage in the EMR failure patient sample group. Only 94 patients had lymphocyte percentage counts at diagnosis information available for analysis. Statistical analysis was performed using the Mann-Whitney U test.
    Figure Legend Snippet: Distinct gene expression profile and enrichment of stem cells signature identified in diagnostic MNCs from patients who failed to achieve EMR. (A) The workflow of our study with regard to the discovery process, including samples from patients with EMR failure (n = 13) vs EMR achievement (n = 83), as defined by BCR-ABL1 percentage at 3 months. (B) Volcano plot demonstrating the effect of log2 fold change (FC) on the x-axis vs −log10 P value on the y-axis. Red circles indicate significant genes (FDR P < .05 and log2 FC > 0.6) with increased gene expression in the EMR failure patient group. Green circles indicate significant genes (FDR P < .05 and log2 FC < −0.6) with decreased gene expression in the EMR failure patient group. (C) Heatmap demonstrating the distinct gene expression patterns based on all significant probes (n = 502; FDR P < .05 and log2 FC > |0.6|). Orange represents increased gene expression level, and blue represents decreased gene expression level. The heatmap was generated using the pheatmap package. (D) GSEA indicates enrichment of stem cell signaling, cell cycle, and immune response/T lymphocytes in the EMR failure patient samples (BCR-ABL1 >10% IS at 3 months) compared with the EMR achievement patient samples (BCR-ABL1 ≤10% IS at 3 months). Blue bars represent cell cycle–related data sets. Red bars represent stem cell–related data sets. Green bars represent immune response/T lymphocyte–related signatures. Regarding normalized enrichment score (NES), positive score indicates positive enrichment in samples from patients who failed to achieve EMR, and negative score indicates enrichment in samples from patients who achieved EMR. (E) Boxplot displaying the differential blast percentage counts at diagnosis, indicating a significantly higher percentage in the samples collected from patients who failed to achieve EMR. Only 91 patients had differential blast percentage counts at diagnosis information available for analysis. (F) Boxplot displaying the lymphocyte percentage counts at diagnosis, indicating a significantly lower percentage in the EMR failure patient sample group. Only 94 patients had lymphocyte percentage counts at diagnosis information available for analysis. Statistical analysis was performed using the Mann-Whitney U test.

    Techniques Used: Gene Expression, Diagnostic Assay, Generated, Biomarker Discovery, MANN-WHITNEY

    Related Articles

    Microarray:

    Article Title: Gene expression signature that predicts early molecular response failure in chronic-phase CML patients on frontline imatinib
    Article Snippet: .. 27 , 28 GEP microarray analysis Genome-wide GEP was performed using the Illumina Human HT-12v4 platform (containing 47 323 probes) at the Australian Genome Research Facility (Melbourne, VIC, Australia). ..

    Genome Wide:

    Article Title: Gene expression signature that predicts early molecular response failure in chronic-phase CML patients on frontline imatinib
    Article Snippet: .. 27 , 28 GEP microarray analysis Genome-wide GEP was performed using the Illumina Human HT-12v4 platform (containing 47 323 probes) at the Australian Genome Research Facility (Melbourne, VIC, Australia). ..



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    Distinct <t>gene</t> <t>expression</t> <t>profile</t> and enrichment of stem cells signature identified in diagnostic MNCs from patients who failed to achieve EMR. (A) The workflow of our study with regard to the discovery process, including samples from patients with EMR failure (n = 13) vs EMR achievement (n = 83), as defined by BCR-ABL1 percentage at 3 months. (B) Volcano plot demonstrating the effect of log2 fold change (FC) on the x-axis vs −log10 P value on the y-axis. Red circles indicate significant genes (FDR P < .05 and log2 FC > 0.6) with increased gene expression in the EMR failure patient group. Green circles indicate significant genes (FDR P < .05 and log2 FC < −0.6) with decreased gene expression in the EMR failure patient group. (C) Heatmap demonstrating the distinct gene expression patterns based on all significant probes (n = 502; FDR P < .05 and log2 FC > |0.6|). Orange represents increased gene expression level, and blue represents decreased gene expression level. The heatmap was generated using the pheatmap package. (D) GSEA indicates enrichment of stem cell signaling, cell cycle, and immune response/T lymphocytes in the EMR failure patient samples (BCR-ABL1 >10% IS at 3 months) compared with the EMR achievement patient samples (BCR-ABL1 ≤10% IS at 3 months). Blue bars represent cell cycle–related data sets. Red bars represent stem cell–related data sets. Green bars represent immune response/T lymphocyte–related signatures. Regarding normalized enrichment score (NES), positive score indicates positive enrichment in samples from patients who failed to achieve EMR, and negative score indicates enrichment in samples from patients who achieved EMR. (E) Boxplot displaying the differential blast percentage counts at diagnosis, indicating a significantly higher percentage in the samples collected from patients who failed to achieve EMR. Only 91 patients had differential blast percentage counts at diagnosis information available for analysis. (F) Boxplot displaying the lymphocyte percentage counts at diagnosis, indicating a significantly lower percentage in the EMR failure patient sample group. Only 94 patients had lymphocyte percentage counts at diagnosis information available for analysis. Statistical analysis was performed using the Mann-Whitney U test.
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    Distinct <t>gene</t> <t>expression</t> <t>profile</t> and enrichment of stem cells signature identified in diagnostic MNCs from patients who failed to achieve EMR. (A) The workflow of our study with regard to the discovery process, including samples from patients with EMR failure (n = 13) vs EMR achievement (n = 83), as defined by BCR-ABL1 percentage at 3 months. (B) Volcano plot demonstrating the effect of log2 fold change (FC) on the x-axis vs −log10 P value on the y-axis. Red circles indicate significant genes (FDR P < .05 and log2 FC > 0.6) with increased gene expression in the EMR failure patient group. Green circles indicate significant genes (FDR P < .05 and log2 FC < −0.6) with decreased gene expression in the EMR failure patient group. (C) Heatmap demonstrating the distinct gene expression patterns based on all significant probes (n = 502; FDR P < .05 and log2 FC > |0.6|). Orange represents increased gene expression level, and blue represents decreased gene expression level. The heatmap was generated using the pheatmap package. (D) GSEA indicates enrichment of stem cell signaling, cell cycle, and immune response/T lymphocytes in the EMR failure patient samples (BCR-ABL1 >10% IS at 3 months) compared with the EMR achievement patient samples (BCR-ABL1 ≤10% IS at 3 months). Blue bars represent cell cycle–related data sets. Red bars represent stem cell–related data sets. Green bars represent immune response/T lymphocyte–related signatures. Regarding normalized enrichment score (NES), positive score indicates positive enrichment in samples from patients who failed to achieve EMR, and negative score indicates enrichment in samples from patients who achieved EMR. (E) Boxplot displaying the differential blast percentage counts at diagnosis, indicating a significantly higher percentage in the samples collected from patients who failed to achieve EMR. Only 91 patients had differential blast percentage counts at diagnosis information available for analysis. (F) Boxplot displaying the lymphocyte percentage counts at diagnosis, indicating a significantly lower percentage in the EMR failure patient sample group. Only 94 patients had lymphocyte percentage counts at diagnosis information available for analysis. Statistical analysis was performed using the Mann-Whitney U test.
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    Distinct gene expression profile and enrichment of stem cells signature identified in diagnostic MNCs from patients who failed to achieve EMR. (A) The workflow of our study with regard to the discovery process, including samples from patients with EMR failure (n = 13) vs EMR achievement (n = 83), as defined by BCR-ABL1 percentage at 3 months. (B) Volcano plot demonstrating the effect of log2 fold change (FC) on the x-axis vs −log10 P value on the y-axis. Red circles indicate significant genes (FDR P < .05 and log2 FC > 0.6) with increased gene expression in the EMR failure patient group. Green circles indicate significant genes (FDR P < .05 and log2 FC < −0.6) with decreased gene expression in the EMR failure patient group. (C) Heatmap demonstrating the distinct gene expression patterns based on all significant probes (n = 502; FDR P < .05 and log2 FC > |0.6|). Orange represents increased gene expression level, and blue represents decreased gene expression level. The heatmap was generated using the pheatmap package. (D) GSEA indicates enrichment of stem cell signaling, cell cycle, and immune response/T lymphocytes in the EMR failure patient samples (BCR-ABL1 >10% IS at 3 months) compared with the EMR achievement patient samples (BCR-ABL1 ≤10% IS at 3 months). Blue bars represent cell cycle–related data sets. Red bars represent stem cell–related data sets. Green bars represent immune response/T lymphocyte–related signatures. Regarding normalized enrichment score (NES), positive score indicates positive enrichment in samples from patients who failed to achieve EMR, and negative score indicates enrichment in samples from patients who achieved EMR. (E) Boxplot displaying the differential blast percentage counts at diagnosis, indicating a significantly higher percentage in the samples collected from patients who failed to achieve EMR. Only 91 patients had differential blast percentage counts at diagnosis information available for analysis. (F) Boxplot displaying the lymphocyte percentage counts at diagnosis, indicating a significantly lower percentage in the EMR failure patient sample group. Only 94 patients had lymphocyte percentage counts at diagnosis information available for analysis. Statistical analysis was performed using the Mann-Whitney U test.

    Journal: Blood Advances

    Article Title: Gene expression signature that predicts early molecular response failure in chronic-phase CML patients on frontline imatinib

    doi: 10.1182/bloodadvances.2019000195

    Figure Lengend Snippet: Distinct gene expression profile and enrichment of stem cells signature identified in diagnostic MNCs from patients who failed to achieve EMR. (A) The workflow of our study with regard to the discovery process, including samples from patients with EMR failure (n = 13) vs EMR achievement (n = 83), as defined by BCR-ABL1 percentage at 3 months. (B) Volcano plot demonstrating the effect of log2 fold change (FC) on the x-axis vs −log10 P value on the y-axis. Red circles indicate significant genes (FDR P < .05 and log2 FC > 0.6) with increased gene expression in the EMR failure patient group. Green circles indicate significant genes (FDR P < .05 and log2 FC < −0.6) with decreased gene expression in the EMR failure patient group. (C) Heatmap demonstrating the distinct gene expression patterns based on all significant probes (n = 502; FDR P < .05 and log2 FC > |0.6|). Orange represents increased gene expression level, and blue represents decreased gene expression level. The heatmap was generated using the pheatmap package. (D) GSEA indicates enrichment of stem cell signaling, cell cycle, and immune response/T lymphocytes in the EMR failure patient samples (BCR-ABL1 >10% IS at 3 months) compared with the EMR achievement patient samples (BCR-ABL1 ≤10% IS at 3 months). Blue bars represent cell cycle–related data sets. Red bars represent stem cell–related data sets. Green bars represent immune response/T lymphocyte–related signatures. Regarding normalized enrichment score (NES), positive score indicates positive enrichment in samples from patients who failed to achieve EMR, and negative score indicates enrichment in samples from patients who achieved EMR. (E) Boxplot displaying the differential blast percentage counts at diagnosis, indicating a significantly higher percentage in the samples collected from patients who failed to achieve EMR. Only 91 patients had differential blast percentage counts at diagnosis information available for analysis. (F) Boxplot displaying the lymphocyte percentage counts at diagnosis, indicating a significantly lower percentage in the EMR failure patient sample group. Only 94 patients had lymphocyte percentage counts at diagnosis information available for analysis. Statistical analysis was performed using the Mann-Whitney U test.

    Article Snippet: 27 , 28 GEP microarray analysis Genome-wide GEP was performed using the Illumina Human HT-12v4 platform (containing 47 323 probes) at the Australian Genome Research Facility (Melbourne, VIC, Australia).

    Techniques: Gene Expression, Diagnostic Assay, Generated, Biomarker Discovery, MANN-WHITNEY