microarray platform (hg-u133a  (Thermo Fisher)

Journal: Human Reproduction Update

Article Title: BCL6 , a key oncogene, in the placenta, pre-eclampsia and endometriosis

doi: 10.1093/humupd/dmac027

Figure Lengend Snippet: BCL6 expression in human pre-eclamptic placentas.

Article Snippet: Winn et al. (2009) , n = 11 preterm labor with no evidence of infection (30.2 ± 7.1 wk, range 24–36, 18% CS and 100% labor). n = 12 severe PE (30.7 ± 9.1 wk, range 24–36, 50% CS and 83% labor). , Microarray platform high-density HG-U133A and HGU133B GeneChips (Affymetrix, Santa Clara, CA); GEO accession number: GSE14722. , 55 genes were differentially expressed in PE placentas, including upregulated BCL6, with a fold change of 1.69..

Techniques: Expressing, Microarray, Infection, RNA Sequencing Assay, Sequencing

Journal: BMC Genomics

Article Title: Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization

doi: 10.1186/1471-2164-15-S12-S8

Figure Lengend Snippet: A comparison of expression profiles obtained using two different Affymetrix HG-U133A probesets mapped to RIPK2 gene .

Article Snippet: Here we evaluate the prevalence of discordant expression in data collected using Affymetrix HG-U133A microarray platform.

Techniques: Expressing

Journal: BMC Genomics

Article Title: Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization

doi: 10.1186/1471-2164-15-S12-S8

Figure Lengend Snippet: Probeset composition per gene in Affymetrix U133A microarray after reannotation .

Article Snippet: Here we evaluate the prevalence of discordant expression in data collected using Affymetrix HG-U133A microarray platform.

Techniques: Microarray

Journal: BMC Genomics

Article Title: Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization

doi: 10.1186/1471-2164-15-S12-S8

Figure Lengend Snippet: The distribution of correlation coefficients values for a subset of genes/gene groups matched by two different probesets . Pearson's product-moment correlation coefficient r is on the x-axis and Spearman's rank correlation coefficient ρ is on the y-axis. Each dot represents correlation between expression values obtained with two different probesets corresponding to one gene on the Affymetrix U133A microarray in GSE1133 dataset. Black lines mark the quadrants that distinguish sets of genes behaving in one or another distinct way that sets them apart from each other. The quadrants were drawn according to correlation coefficient values. Values above 0.7 and below 0.3 were considered cut-offs. Number of genes that fell into each quadrant is shown in red color. Question marks represent the areas populated by genes with less deviant behavior that is evident from milder degree of decrepancy between correlation coefficients calculated using Pearson's coefficient r and Spearman's coefficient ρ . Dark red dashed line represents linear regression line and its equation is in the bottom right corner of the plot.

Article Snippet: Here we evaluate the prevalence of discordant expression in data collected using Affymetrix HG-U133A microarray platform.

Techniques: Expressing, Microarray

Journal: BMC Genomics

Article Title: Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization

doi: 10.1186/1471-2164-15-S12-S8

Figure Lengend Snippet: Plot of means and coefficients of variation of expression data obtained with different probe sets annotated to one gene with Spearman's correlation ρ ≥ 0 .9 (upper panel) and 0.7 ≤ ρ < 0.9 (lower panel). Each dot represents means of expression data (left part) or coefficients of correlation (right part) obtained with two probesets corresponding to one gene on the Affymetrix U133A microarray in GSE1133 dataset (probe set 1 on the x-axis and probe set 2 on the y-axis). Black line represents linear regression line and its equation is in the top left corner of plot. See also Additional file Supplementary Fig S4.

Article Snippet: Here we evaluate the prevalence of discordant expression in data collected using Affymetrix HG-U133A microarray platform.

Techniques: Expressing, Microarray