ArticleNucleic acids research2005
Protocols for the assurance of microarray data quality and process control.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- 2,3,7,8-Tetrachlorodibenzo-p-Dioxin Alters Lipid Metabolism and Depletes Immune Cell Populations in the Jejunum of C57BL/6 Mice.Toxicological sciences : an official journal of the Society of Toxicology · 2015Article
- Loss of Hif-2α Rescues the Hif-1α Deletion Phenotype of Neonatal Respiratory Distress In Mice.PloS one · 2015Article
- AP-1/Fos-TGase2 axis mediates wounding-induced Plasmodium falciparum killing in Anopheles gambiae.The Journal of biological chemistry · 2013Article
- Comparative analysis of temporal and dose-dependent TCDD-elicited gene expression in human, mouse, and rat primary hepatocytes.Toxicological sciences : an official journal of the Society of Toxicology · 2013Article
- Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.PloS one · 2013Article
- Plastids are major regulators of light signaling in Arabidopsis.Plant physiology · 2012Article
- Non-additive hepatic gene expression elicited by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and 2,2',4,4',5,5'-hexachlorobiphenyl (PCB153) co-treatment in C57BL/6 mice.Toxicology and applied pharmacology · 2011Article
- Differences in TCDD-elicited gene expression profiles in human HepG2, mouse Hepa1c1c7 and rat H4IIE hepatoma cells.BMC genomics · 2011Article
- Automated dose-response analysis and comparative toxicogenomic evaluation of the hepatic effects elicited by TCDD, TCDF, and PCB126 in C57BL/6 mice.Toxicological sciences : an official journal of the Society of Toxicology · 2010Article
- PCB153-elicited hepatic responses in the immature, ovariectomized C57BL/6 mice: comparative toxicogenomic effects of dioxin and non-dioxin-like ligands.Toxicology and applied pharmacology · 2010Article
- Unsupervised assessment of microarray data quality using a Gaussian mixture model.BMC bioinformatics · 2009Article
- An integrated bioinformatics approach to improve two-color microarray quality-control: impact on biological conclusions.Genes & nutrition · 2009Article
- Tamoxifen-elicited uterotrophy: cross-species and cross-ligand analysis of the gene expression program.BMC medical genomics · 2009Article
- Toxicogenomic biomarkers for liver toxicity.Journal of toxicologic pathology · 2009Article
- Quality assessment of microarray data in a multicenter study.Diagnostic molecular pathology : the American journal of surgical pathology, part B · 2009Article
- MOF: an R function to detect outlier microarray.Genomics, proteomics & bioinformatics · 2008Article
- Comparative temporal and dose-dependent morphological and transcriptional uterine effects elicited by tamoxifen and ethynylestradiol in immature, ovariectomized mice.BMC genomics · 2007Article
- Detecting outlier microarray arrays by correlation and percentage of outliers spots.Cancer informatics · 2007Article
- Analysis of the quality of contact-pin fabricated oligonucleotide microarrays.Molecular biotechnology · 2006Article
- In vivo-in vitro toxicogenomic comparison of TCDD-elicited gene expression in Hepa1c1c7 mouse hepatoma cells and C57BL/6 hepatic tissue.BMC genomics · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Microarrays represent a powerful technology that provides the ability to simultaneously measure the expression of thousands of genes. However, it is a multi-step process with numerous potential sources of variation that can compromise data analysis and interpretation if left uncontrolled, necessitating the development of quality control protocols to ensure assay consistency and high-quality data. In response to emerging standards, such as the minimum information about a microarray experiment standard, tools are required to ascertain the quality and reproducibility of results within and across studies. To this end, an intralaboratory quality control protocol for two color, spotted microarrays was developed using cDNA microarrays from in vivo and in vitro dose-response and time-course studies. The protocol combines: (i) diagnostic plots monitoring the degree of feature saturation, global feature and background intensities, and feature misalignments with (ii) plots monitoring the intensity distributions within arrays with (iii) a support vector machine (SVM) model. The protocol is applicable to any laboratory with sufficient datasets to establish historical high- and low-quality data.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.