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rna expression profiling huex microarray  (INFINIUM Inc)

 
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    INFINIUM Inc rna expression profiling huex microarray
    Adrenal vs thoracic tumor copy number association analysis. A) Meta-analysis by nonoverlapping 1-Mb tiles. The y-axis reflects an inverse variance-weighted meta-analysis across four datasets—single nucleotide polymorphism (SNP) <t>microarray,</t> whole genome sequencing, whole exome sequencing, and gene panel sequencing cohorts—of average log-ratio (tumor normalized to normal) differences between adrenal vs thoracic cases divided by SD (z score). A positive z score (red) implies that the relative copy number is higher in adrenal vs thoracic cases and a negative z score (blue) implies the opposite. The inner dashed line illustrates the z score corresponding to a nominal P value cut point of .05, and the outer dotted line illustrates the z score corresponding to a multiple test-adjusted false discovery rate (FDR) cut point of 0.05. The 1-Mb bin containing MYCN is labeled, because it is the only focal copy number alteration to reach statistical significance. B) Meta-analysis by chromosome arm. “Avg Adrenal” and “Avg Thoracic” denote a weighted average copy number log-ratio for adrenal and thoracic cases, respectively. More positive/red values reflect regions of greater copy number gain and more negative/blue values reflect regions of greater copy number loss. From the difference of these values (Avg Difference), a z score and two-tailed P value were computed by inverse-variance meta-analysis. The FDR was controlled by the Benjamini-Hochberg method. Results with multiple test-adjusted statistical significance at FDR less than 0.05 are bolded.
    Rna Expression Profiling Huex Microarray, supplied by INFINIUM 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/rna+microarray/rna+expression+profiling+huex+microarray/pmc06855946-178-42-62
    Average 90 stars, based on 1 article reviews
    rna expression profiling huex microarray - by Bioz Stars, 2026-09
    90/100 stars

    Images

    1) Product Images from "Differences in Genomic Profiles and Outcomes Between Thoracic and Adrenal Neuroblastoma"

    Article Title: Differences in Genomic Profiles and Outcomes Between Thoracic and Adrenal Neuroblastoma

    Journal: JNCI Journal of the National Cancer Institute

    doi: 10.1093/jnci/djz027

    Adrenal vs thoracic tumor copy number association analysis. A) Meta-analysis by nonoverlapping 1-Mb tiles. The y-axis reflects an inverse variance-weighted meta-analysis across four datasets—single nucleotide polymorphism (SNP) microarray, whole genome sequencing, whole exome sequencing, and gene panel sequencing cohorts—of average log-ratio (tumor normalized to normal) differences between adrenal vs thoracic cases divided by SD (z score). A positive z score (red) implies that the relative copy number is higher in adrenal vs thoracic cases and a negative z score (blue) implies the opposite. The inner dashed line illustrates the z score corresponding to a nominal P value cut point of .05, and the outer dotted line illustrates the z score corresponding to a multiple test-adjusted false discovery rate (FDR) cut point of 0.05. The 1-Mb bin containing MYCN is labeled, because it is the only focal copy number alteration to reach statistical significance. B) Meta-analysis by chromosome arm. “Avg Adrenal” and “Avg Thoracic” denote a weighted average copy number log-ratio for adrenal and thoracic cases, respectively. More positive/red values reflect regions of greater copy number gain and more negative/blue values reflect regions of greater copy number loss. From the difference of these values (Avg Difference), a z score and two-tailed P value were computed by inverse-variance meta-analysis. The FDR was controlled by the Benjamini-Hochberg method. Results with multiple test-adjusted statistical significance at FDR less than 0.05 are bolded.
    Figure Legend Snippet: Adrenal vs thoracic tumor copy number association analysis. A) Meta-analysis by nonoverlapping 1-Mb tiles. The y-axis reflects an inverse variance-weighted meta-analysis across four datasets—single nucleotide polymorphism (SNP) microarray, whole genome sequencing, whole exome sequencing, and gene panel sequencing cohorts—of average log-ratio (tumor normalized to normal) differences between adrenal vs thoracic cases divided by SD (z score). A positive z score (red) implies that the relative copy number is higher in adrenal vs thoracic cases and a negative z score (blue) implies the opposite. The inner dashed line illustrates the z score corresponding to a nominal P value cut point of .05, and the outer dotted line illustrates the z score corresponding to a multiple test-adjusted false discovery rate (FDR) cut point of 0.05. The 1-Mb bin containing MYCN is labeled, because it is the only focal copy number alteration to reach statistical significance. B) Meta-analysis by chromosome arm. “Avg Adrenal” and “Avg Thoracic” denote a weighted average copy number log-ratio for adrenal and thoracic cases, respectively. More positive/red values reflect regions of greater copy number gain and more negative/blue values reflect regions of greater copy number loss. From the difference of these values (Avg Difference), a z score and two-tailed P value were computed by inverse-variance meta-analysis. The FDR was controlled by the Benjamini-Hochberg method. Results with multiple test-adjusted statistical significance at FDR less than 0.05 are bolded.

    Techniques Used: Microarray, Sequencing, Labeling, Two Tailed Test

    Unbiased clustering analysis of functional genomic and DNA methylation data in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) cohort. Heatmaps and hierarchical clustering for all adrenal and thoracic (A) HuEx RNA microarray samples and (B) DNA methylation microarray samples. Rows reflect independent patient profiles and columns reflect the 200 probesets with the highest variance after (A) log2 transformation of RNA probe intensity and (B) logit transformation of methylation beta values. Columns are mean-centered and normalized by SD (z score transformation) and illustrated on a blue-yellow scale. Additional colored boxes illustrate clinical annotations for each patient according to the legend (white = missing annotation).
    Figure Legend Snippet: Unbiased clustering analysis of functional genomic and DNA methylation data in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) cohort. Heatmaps and hierarchical clustering for all adrenal and thoracic (A) HuEx RNA microarray samples and (B) DNA methylation microarray samples. Rows reflect independent patient profiles and columns reflect the 200 probesets with the highest variance after (A) log2 transformation of RNA probe intensity and (B) logit transformation of methylation beta values. Columns are mean-centered and normalized by SD (z score transformation) and illustrated on a blue-yellow scale. Additional colored boxes illustrate clinical annotations for each patient according to the legend (white = missing annotation).

    Techniques Used: Functional Assay, DNA Methylation Assay, Microarray, Transformation Assay, Methylation



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    Image Search Results


    Volcano plots showing the mature miRNAs differentially expressed in the TraxE126A mutants compared to wildtype littermates as identified by (A) miRNA sequencing and (B) miRNA microarray. Volcano plots showing the differentially expressed small RNA species identified using microarray analysis including (C) Precursor miRNAs (pre-miRNAs), (D) Small nucleolar RNAs (snoRNAs), (E) mature tRNAs and (F) tRNA-derived small RNAs (tsRNAs). In all the plots, the upregulated and downregulated miRNAs (false discovery rate, FDR <0.050 and log 2 fold change ≥0.200) are highlighted in red and blue, respectively. (TraxE126A, n=4; WT, n=5, all males). Largest changes were seen in tsRNA levels (majority are 5’-fragments) and mature miRNAs.

    Journal: bioRxiv

    Article Title: Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory

    doi: 10.1101/2025.07.10.663777

    Figure Lengend Snippet: Volcano plots showing the mature miRNAs differentially expressed in the TraxE126A mutants compared to wildtype littermates as identified by (A) miRNA sequencing and (B) miRNA microarray. Volcano plots showing the differentially expressed small RNA species identified using microarray analysis including (C) Precursor miRNAs (pre-miRNAs), (D) Small nucleolar RNAs (snoRNAs), (E) mature tRNAs and (F) tRNA-derived small RNAs (tsRNAs). In all the plots, the upregulated and downregulated miRNAs (false discovery rate, FDR <0.050 and log 2 fold change ≥0.200) are highlighted in red and blue, respectively. (TraxE126A, n=4; WT, n=5, all males). Largest changes were seen in tsRNA levels (majority are 5’-fragments) and mature miRNAs.

    Article Snippet: The labeled RNA species are then hybridized onto Arraystar Small RNA Expression Microarray (8×15K format), scanned by an Agilent G2505C scanner followed by data processing and analysis.

    Techniques: Sequencing, Microarray, Derivative Assay

    (A) Venn diagram showing the overlap between mature miRNAs identified using miRNA sequencing and microarray analysis (with FDR<0.050 and log 2 fold change ≥0.200). A total of 12 miRNAs (10 upregulated and 2 downregulated) were found to be common and were used for target prediction using miRDB database. (B) An upset plot showing the shared and unique predicted mRNA target profiles in the miRDB database for the 12 common miRNAs. Only targets with miRDB Target Score ≥60 are included. (C) Top 15 KEGG pathways and (D) Gene Ontology (GO) Biological Process terms from the functional enrichment analysis of the predicted targets of the 12 common miRNAs performed using DAVID database.

    Journal: bioRxiv

    Article Title: Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory

    doi: 10.1101/2025.07.10.663777

    Figure Lengend Snippet: (A) Venn diagram showing the overlap between mature miRNAs identified using miRNA sequencing and microarray analysis (with FDR<0.050 and log 2 fold change ≥0.200). A total of 12 miRNAs (10 upregulated and 2 downregulated) were found to be common and were used for target prediction using miRDB database. (B) An upset plot showing the shared and unique predicted mRNA target profiles in the miRDB database for the 12 common miRNAs. Only targets with miRDB Target Score ≥60 are included. (C) Top 15 KEGG pathways and (D) Gene Ontology (GO) Biological Process terms from the functional enrichment analysis of the predicted targets of the 12 common miRNAs performed using DAVID database.

    Article Snippet: The labeled RNA species are then hybridized onto Arraystar Small RNA Expression Microarray (8×15K format), scanned by an Agilent G2505C scanner followed by data processing and analysis.

    Techniques: Sequencing, Microarray, Functional Assay