Journal: The New England journal of medicine

Article Title: Adaptive Randomization of Veliparib–Carboplatin Treatment in Breast Cancer

doi: 10.1056/NEJMoa1513749

Figure Lengend Snippet: Patients are screened for I-SPY 2 eligibility. Eligible patients are adaptively randomized to 12 weekly paclitaxel (and trastuzumab if HER2+) cycles (control) or in combination with one of several experimental agents followed by doxorubicin/cyclophosphamide (AC) × 4, with serial biomarkers (biopsies, blood draw and MRI scans) assessed over the course of their therapy. Only patients with HER2− disease were randomized to the veliparib/carboplatin arm.

Article Snippet: Biomarker assessments include the Agendia 70-gene MammaPrint and TargetPrint HER2 gene expression using the Agendia 44K full genome microarray and reverse phase phosphoprotein array.

Techniques:

Journal: The New England journal of medicine

Article Title: Adaptive Randomization of Veliparib–Carboplatin Treatment in Breast Cancer

doi: 10.1056/NEJMoa1513749

Figure Lengend Snippet: Only patients with HER2-negative disease were eligible for randomization to the VC arm. Patients were categorized as received allocated invention if they received at least one dose of experimental (or control) therapy.

Article Snippet: Biomarker assessments include the Agendia 70-gene MammaPrint and TargetPrint HER2 gene expression using the Agendia 44K full genome microarray and reverse phase phosphoprotein array.

Techniques:

Journal: The New England journal of medicine

Article Title: Adaptive Randomization of Veliparib–Carboplatin Treatment in Breast Cancer

doi: 10.1056/NEJMoa1513749

Figure Lengend Snippet: Estimated pCR Rate for the signatures evaluated for V/C vs. concurrent HER2-negative control.

Article Snippet: Biomarker assessments include the Agendia 70-gene MammaPrint and TargetPrint HER2 gene expression using the Agendia 44K full genome microarray and reverse phase phosphoprotein array.

Techniques: Negative Control

Journal: The New England journal of medicine

Article Title: Adaptive Randomization of Veliparib–Carboplatin Treatment in Breast Cancer

doi: 10.1056/NEJMoa1513749

Figure Lengend Snippet: Final predictive probabilities

Article Snippet: Biomarker assessments include the Agendia 70-gene MammaPrint and TargetPrint HER2 gene expression using the Agendia 44K full genome microarray and reverse phase phosphoprotein array.

Techniques:

Journal: The New England journal of medicine

Article Title: Adaptive Randomization of Veliparib–Carboplatin Treatment in Breast Cancer

doi: 10.1056/NEJMoa1513749

Figure Lengend Snippet: Selected Toxicities

Article Snippet: Biomarker assessments include the Agendia 70-gene MammaPrint and TargetPrint HER2 gene expression using the Agendia 44K full genome microarray and reverse phase phosphoprotein array.

Techniques:

Journal: Annals of Medicine

Article Title: MiR-223-3p regulates erythropoiesis by targeting TGFBR3/Smad signaling pathway in hemoglobin H-Constant Spring disease

doi: 10.1080/07853890.2025.2530690

Figure Lengend Snippet: Comparison of the expression profiles of miRNAs(A-C) and mRNAs (D-F) between HbH-CS patients and healthy controls. (A) Scatter plot showing the distribution of miRNA expression. (B) Volcano plot showing the differential expression of miRNAs. (C) The clustering heatmap showed differentially expressed miRNAs between patients with HbH-CS patients and healthy controls. (D) Scatter plot showing the distribution of mRNA expression. (E) Volcano plot showing the differential expression of mRNAs. (F) The clustering heatmap showed differentially expressed mRNAs between patients with HbH-CS patients and healthy controls.

Article Snippet: MiRNAs associated with hematopoietic cell lineage, apoptosis, and cell cycle were searched in the database, which were stratified by Arraystar miRNA expression profiling microarray data filtered according to p < 0.05 and log FC >1.5.

Techniques: Comparison, Expressing, Quantitative Proteomics

Journal: Annals of Medicine

Article Title: MiR-223-3p regulates erythropoiesis by targeting TGFBR3/Smad signaling pathway in hemoglobin H-Constant Spring disease

doi: 10.1080/07853890.2025.2530690

Figure Lengend Snippet: Bioinformatics analysis. (A) Venn diagram showed stratified operations of miRNAs from the original data and online database. (B) Intersection plot of mRNAs from our previous ArrayStar human mRNA array and miR-223-3p target gene predicted by online database. (C) Prediction plot of miR-223-3p target gene. Yellow circled node, miR-223-3p; blue rectangle type node, mRNA. (D, E) The qRT-PCR was performed to detect the relative expression levels of miR-223-3p (D) and TGFBR3 (E) in the samples from healthy normal subjects and HbH-CS patients. Normal group, n = 17; HbH-CS group, n = 17, mean ± SEM, ** p < 0.01, *** p < 0.001.

Article Snippet: MiRNAs associated with hematopoietic cell lineage, apoptosis, and cell cycle were searched in the database, which were stratified by Arraystar miRNA expression profiling microarray data filtered according to p < 0.05 and log FC >1.5.

Techniques: Quantitative RT-PCR, Expressing

Journal: Journal of Allergy

Article Title: How Can Microarrays Unlock Asthma?

doi: 10.1155/2012/241314

Figure Lengend Snippet: Overview of the production and use of expression microarrays. 3′ Expression arrays use synthetically derived oligo probes with design based on mRNA Databases (RefSeq mRNAs, GenBank mRNAs, and ESTs from dbEST) or cDNA derived from bacterial libraries (see ). Sample mRNA can be labeled using two methods (a) Cy3/Cy5 labeling: sample mRNA is reverse transcribed into cDNA and Cy3 is added to one sample and Cy5 to another. Both labeled samples are hybridized to the same microarray. (b) 3′ IVT array: sample mRNA is reverse transcribed to cDNA using oligo(dT) primers, to provide a template for transcription. Using biotin-conjugated nucleotides, the template cDNA is then converted to amplified RNA (aRNA). The biotin-labeled aRNA samples are then fragmented and hybridized onto 3′ expression arrays. A biotin binding fluorescent stain is added to the microarray after hybridization. (c) Affymetrix HuExon 1.0 ST: sample mRNA is reverse transcribed to cDNA using random primers, to provide a template for transcription. The resulting RNA is then reverse transcribed in the presence of dUTPs which are incorporated occasionally into the cDNA sequence instead of dTTP. An enzyme is then used to cleave the cDNA at the site of dUTP incorporation and fragments are terminally labeled before hybridization onto the array. The microarray is then washed and stained after hybridization.

Article Snippet: In an attempt to identify the role of IL13 and its isotypes in the pathogenesis of allergic asthma, Syed et al. looked at the effect of IL13 and IL13R130Q on ASM using an expression microarray containing 8159 human gene cDNA clones from Research Genetics (IMAGE consortium, Huntsville, AL), Incyte Genomics (Santa Clara, CA) [ ].

Techniques: Expressing, Derivative Assay, Labeling, Reverse Transcription, Microarray, Amplification, Binding Assay, Staining, Hybridization, Sequencing

Journal: Journal of Allergy

Article Title: How Can Microarrays Unlock Asthma?

doi: 10.1155/2012/241314

Figure Lengend Snippet: The GEO accession number for microarray studies conducted on asthma.

Article Snippet: In an attempt to identify the role of IL13 and its isotypes in the pathogenesis of allergic asthma, Syed et al. looked at the effect of IL13 and IL13R130Q on ASM using an expression microarray containing 8159 human gene cDNA clones from Research Genetics (IMAGE consortium, Huntsville, AL), Incyte Genomics (Santa Clara, CA) [ ].

Techniques: Microarray, Gene Expression, Clone Assay, Expressing, Virus, Infection, Functional Assay, Sequencing, Synthesized, Comparison

Journal: Molecular Vision

Article Title: Microarray reveals complement components are regulated in the serum-deprived rat retinal ganglion cell line

doi:

Figure Lengend Snippet: Genes identified in our microarray data and other.

Article Snippet: To identify potential signaling and pathways and gene-regulatory networks that are associated with retinal ganglion cell death,we imported the microarray expression data to PathwayAssist (Iobion, Informatics, LLC).

Techniques: Microarray, Membrane

Journal: Molecular Vision

Article Title: Microarray reveals complement components are regulated in the serum-deprived rat retinal ganglion cell line

doi:

Figure Lengend Snippet: Genes identified in our microarray and compared with other data.

Article Snippet: To identify potential signaling and pathways and gene-regulatory networks that are associated with retinal ganglion cell death,we imported the microarray expression data to PathwayAssist (Iobion, Informatics, LLC).

Techniques: Microarray, Binding Assay

Journal: Molecular Vision

Article Title: Microarray reveals complement components are regulated in the serum-deprived rat retinal ganglion cell line

doi:

Figure Lengend Snippet: Schematic representations of potential signaling pathways involved in serum-deprived retinal ganglion cell-5 cells. Pathways were identified by incorporating the microarray results (differentially expressed genes identified at 8, 24, 48, and 96 h of serum deprivation) into PathwayAssist software. The pathway connects the proteins (blue color) and cell processes together. Three major biological processes of cell survival, apoptosis, and DNA fragmentation, regulated by these genes are represented by yellow color squares.

Article Snippet: To identify potential signaling and pathways and gene-regulatory networks that are associated with retinal ganglion cell death,we imported the microarray expression data to PathwayAssist (Iobion, Informatics, LLC).

Techniques: Protein-Protein interactions, Microarray, Software

Journal: Molecular Vision

Article Title: Microarray reveals complement components are regulated in the serum-deprived rat retinal ganglion cell line

doi:

Figure Lengend Snippet: The biological pathway of the differentially expressed genes at 24, 48, and 96 h serum deprivation. A : Genes downregulated by serum deprivation (blue color). B : Genes upregulated by serum deprivation (violet color). The pathway was constructed on PathwayAssist software by searching for the shortest path to connect the genes of interest by other genes or cell processes with which they interacted through expression or regulation only. Each of these additional nodes has documented relation to apoptosis. The genes highlighted in blue color are the genes identified by microarray analysis, and the genes in red ovals diamonds color are the potential target genes identified with the aid of PathwayAssist.

Article Snippet: To identify potential signaling and pathways and gene-regulatory networks that are associated with retinal ganglion cell death,we imported the microarray expression data to PathwayAssist (Iobion, Informatics, LLC).

Techniques: Construct, Software, Expressing, Microarray

Journal: Molecular Vision

Article Title: Microarray reveals complement components are regulated in the serum-deprived rat retinal ganglion cell line

doi:

Figure Lengend Snippet: Biological pathway for the differentially expressed neuronal cell death genes in serum-deprived retinal ganglion cells. Pathways were identified by incorporating the microarray results (genes which are differentially expressed at 24, 48, and 96 h) into the Pathway Assit software. The pathway was constructed on this software by searching for the shortest path to connect the genes of interest by other genes or cell processes with which they interacted through expression or regulation only. Three major biologic processes are identified (apoptosis, death, and DNA fragmentation) and are represented by yellow rectangles. Blue ovals denote genes identified as neuronal cell death, and red ovals new genes connected to this pathway.

Article Snippet: To identify potential signaling and pathways and gene-regulatory networks that are associated with retinal ganglion cell death,we imported the microarray expression data to PathwayAssist (Iobion, Informatics, LLC).

Techniques: Microarray, Software, Construct, Expressing

Journal: Molecular Vision

Article Title: Microarray reveals complement components are regulated in the serum-deprived rat retinal ganglion cell line

doi:

Figure Lengend Snippet: Comparative evaluation of microarray and real-time RT-PCR results. Twelve genes, identified as differentially expressed in gene arrays and regulated in response to time-dependent serum deprivation, were evaluated with RT-PCR. Values on the y-axis represent the fold change derived from the mean expression value for each gene, and values on the x-axis represent the time course of RGC-5 serum deprivation. Total RNA isolated from these cells was used for both microarray analysis and real-time RT-PCR. The closed circles (rectangle) represent microarray results, whereas the closed squares (circle) represent the quantitative RT-PCR data.

Article Snippet: To identify potential signaling and pathways and gene-regulatory networks that are associated with retinal ganglion cell death,we imported the microarray expression data to PathwayAssist (Iobion, Informatics, LLC).

Techniques: Microarray, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction, Derivative Assay, Expressing, Isolation