Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparability and concordance of replicated microarray data.

ABSTRACT: To measures the comparability and concordance of Illumina microarray, a series of 30 samples of Universal Human Reference RNA (UHRR) were set as controls for every single chip of total 30 Human-Ref V2 BeadChips. The average bead number of the 30 arrays was 42.3±8.1 for any bead type over the 22,184 probes. A high average correlation coefficient (r) value was obtained as 0.9908±0077 relative to each other of the expression intensity values from the 30 duplicate UHRR samples. 30 UHRR (Stratagene; La Jolla, CA) samples were used as controls for each of 30 BeadChips.

ORGANISM(S): Homo sapiens

SUBMITTER: Dong-Yu Wang

PROVIDER: E-GEOD-16984 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A new gene expression signature, the ClinicoMolecular Triad Classification, may improve prediction and prognostication of breast cancer at the time of diagnosis.

Wang Dong-Yu DY Done Susan J SJ McCready David R DR Boerner Scott S Kulkarni Supriya S Leong Wey Liang WL

Breast cancer research : BCR 20110922 5

<h4>Introduction</h4>When making treatment decisions, oncologists often stratify breast cancer (BC) into a low-risk group (low-grade estrogen receptor-positive (ER+)), an intermediate-risk group (high-grade ER+) and a high-risk group that includes Her2+ and triple-negative (TN) tumors (ER-/PR-/Her2-). None of the currently available gene signatures correlates to this clinical classification. In this study, we aimed to develop a test that is practical for oncologists and offers both molecular cha ...[more]

PMID: 21939527

Similar Datasets

Comparability and concordance of replicated microarray data.

Project description:To measures the comparability and concordance of Illumina microarray, a series of 30 samples of Universal Human Reference RNA (UHRR) were set as controls for every single chip of total 30 Human-Ref V2 BeadChips. The average bead number of the 30 arrays was 42.3±8.1 for any bead type over the 22,184 probes. A high average correlation coefficient (r) value was obtained as 0.9908±0077 relative to each other of the expression intensity values from the 30 duplicate UHRR samples.

2011-09-29 | GSE16984 | GEO

Repeatability and comparability of microRNA microarray

2009-05-14 | GSE13860 | GEO

Repeatability and comparability of microRNA microarray

Project description:We compared repeatability and comparability of microRNA microarray using 5 different platforms. and compared microarray data generated from five different microRNA microarray platforms with quantitative RT-PCR. Our data suggested that the most accurate and repeatable methods for microRNA expression profiling are Agilent and Toray, and the numbers of detected microRNA at Toray are more than at Agilent. Keywords: repeatability, comparability, microRNA, microarray We compared repeatability and comparability of microRNA microarray using 5 different platforms (Agilent, Ambion, Exiqon, Invitrogen, and Toray). In addition, we compared microarray data generated from five different microRNA microarray platforms with quantitative RT-PCR.

2010-05-19 | E-GEOD-13860 | biostudies-arrayexpress

Comparability and concordance of replicated microarray data

| S-ECPF-GEOD-16984 | biostudies-other

Cross-platform comparability of microarray data

Project description:To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms and methods to accommodate this variability. RNA expression data were generated in seven laboratories, comparing two standard RNA samples using twelve microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories dramatically increased when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Nonetheless, concordance could be found across different laboratories and platforms when data were analyzed in terms of enriched Gene Ontology categories. These findings indicate that microarray results generated by multiple sites and platforms can be comparable, and that multi-investigator teams will maximize data comparability by adopting a common platform and a common set of procedures to generate compatible data. Keywords: other

2005-04-21 | GSE2458 | GEO

Cross-platform comparability of microarray data

2010-06-10 | E-GEOD-2458 | biostudies-arrayexpress

DNA methylation profiling of polycystic ovarian syndrome (PCOS)

Project description:Genome-wide DNA methylation analysis on PCOS using Illumina HumanMethylation 450K BeadChips in 30 PCOS patients and 30 healthy controls

2016-08-22 | GSE80468 | GEO

Ecotoxicogenomics: interlaboratory comparability of microarray data [LabA_WB]

Project description:Additional toxicity testing and regulation are needed as the number of compounds chronically released into aquatic coastal environments increases. Decision makers require comprehensive and efficient screening tools to detect adverse biological effects and to identify their cause. Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, identifying sub-lethal organismal responses and identifying contaminant classes underlying observed toxicity. Before transcriptomic information is used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps that impact the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories. Estuarine amphipods were exposed to cyfluthrin-spiked or control sediments for 10 days. Two sample types were generated: the first consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the second type consisted of exposed and control whole body amphipods (WB) from which RNA was extracted by each laboratory. A subset of genes were consistently identified as differentially expressed across all laboratories and sample types. Genes with the highest magnitude of differential expression (> 2 fold) were more likely to be consistently identified as differentially expressed across laboratories. Differentially expressed data had a higher degree of concordance across all laboratories (W = 0.7) in samples with similar RNA quality (Ex) when compared to WB samples (W = 0.5). Our results revealed that several factors can affect data comparability including RNA sample preparation, labeling, instrumentation and technical expertise.

2015-01-26 | GSE64203 | GEO

Ecotoxicogenomics: interlaboratory comparability of microarray data [LabA_Ex]

2015-01-26 | GSE64202 | GEO

Ecotoxicogenomics: interlaboratory comparability of microarray data [LabF_Ex]

2015-01-26 | GSE64211 | GEO