ArticleBMC genomics2010
Consistent annotation of gene expression arrays.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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.
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Who cites it
13 citing papers in PubMed, 30 citations in OpenAlex.
- Article
- rePROBE: Workflow for Revised Probe Assignment and Updated Probe-set Annotation in Microarrays.Genomics, proteomics & bioinformatics · 2021Article
- Ensembl regulation resources.Database : the journal of biological databases and curation · 2016Article
- Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization.BMC genomics · 2014Article
- Long-term IL-33-producing epithelial progenitor cells in chronic obstructive lung disease.The Journal of clinical investigation · 2013Article
- Differential network analysis for the identification of condition-specific pathway activity and regulation.Bioinformatics (Oxford, England) · 2013Article
- Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks.BMC research notes · 2013Article
- Differential gene expression at the maternal-fetal interface in preeclampsia is influenced by gestational age.PloS one · 2013Article
- Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.BMC research notes · 2012Article
- Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function.Nucleic acids research · 2011Article
- Strategies for aggregating gene expression data: the collapseRows R function.BMC bioinformatics · 2011Article
- Ensembl 2011.Nucleic acids research · 2011Article
- Ensembl BioMarts: a hub for data retrieval across taxonomic space.Database : the journal of biological databases and curation · 2011Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundGene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome. Effectively translating the results from the microarray into a biological interpretation requires an accurate mapping between the probesets on the array and the genes that they are targeting. Although major array manufacturers provide annotations of their gene expression arrays, the methods used by various manufacturers are different and the annotations are difficult to keep up to date in the rapidly changing world of biological sequence databases.
resultsWe have created a consistent microarray annotation protocol applicable to all of the major array manufacturers. We constantly keep our annotations updated with the latest Ensembl Gene predictions, and thus cross-referenced with a large number of external biomedical sequence database identifiers. We show that these annotations are accurate and address in detail reasons for the minority of probesets that cannot be annotated. Annotations are publicly accessible through the Ensembl Genome Browser and programmatically through the Ensembl Application Programming Interface. They are also seamlessly integrated into the BioMart data-mining tool and the biomaRt package of BioConductor.
conclusionsConsistent, accurate and updated gene expression array annotations remain critical for biological research. Our annotations facilitate accurate biological interpretation of gene expression profiles.
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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.