ArticlePloS one2006
Probe selection and expression index computation of Affymetrix Exon Arrays.
Article in PloS one, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 77 citations in OpenAlex.
- Alternative splicing in endothelial cells: novel therapeutic opportunities in cancer angiogenesis.Journal of experimental & clinical cancer research : CR · 2020Review
- Exon Array Biomarkers for the Differential Diagnosis of Schizophrenia and Bipolar Disorder.Molecular neuropsychiatry · 2018Article
- Antisense transcription at the TRPM2 locus as a novel prognostic marker and therapeutic target in prostate cancer.Oncogene · 2015Article
- Splice isoforms of phosducin-like protein control the expression of heterotrimeric G proteins.The Journal of biological chemistry · 2013Article
- A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.Nucleic acids research · 2013Article
- Estimation of data-specific constitutive exons with RNA-Seq data.BMC bioinformatics · 2013Article
- JETTA: junction and exon toolkits for transcriptome analysis.Bioinformatics (Oxford, England) · 2012Article
- Myocardial alternative RNA splicing and gene expression profiling in early stage hypoplastic left heart syndrome.PloS one · 2012Article
- Article
- Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content.Genome biology · 2011Article
- Context-dependent robustness to 5' splice site polymorphisms in human populations.Human molecular genetics · 2011Article
- A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species.Nucleic acids research · 2011Article
- Exon array analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer.BMC genomics · 2010Article
- Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays.BMC bioinformatics · 2010Article
- Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome.PLoS biology · 2010Article
- Evolution of alternative splicing in primate brain transcriptomes.Human molecular genetics · 2010Article
- Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays.BMC bioinformatics · 2010Article
- Cross-platform expression microarray performance in a mouse model of mitochondrial disease therapy.Molecular genetics and metabolism · 2010Article
- The nuclear experience of CPEB: implications for RNA processing and translational control.RNA (New York, N.Y.) · 2010Article
- MADS+: discovery of differential splicing events from Affymetrix exon junction array data.Bioinformatics (Oxford, England) · 2010Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThere is great current interest in developing microarray platforms for measuring mRNA abundance at both gene level and exon level. The Affymetrix Exon Array is a new high-density gene expression microarray platform, with over six million probes targeting all annotated and predicted exons in a genome. An important question for the analysis of exon array data is how to compute overall gene expression indexes. Because of the complexity of the design of exon array probes, this problem is different in nature from summarizing gene-level expression from traditional 3' expression arrays. METHODOLOGY/PRINCIPAL
findingsIn this manuscript, we use exon array data from 11 human tissues to study methods for computing gene-level expression. We showed that for most genes there is a subset of exon array probes having highly correlated intensities across multiple samples. We suggest that these probes could be used as reliable indicators of overall gene expression levels. We developed a probe selection algorithm to select such a subset of highly correlated probes for each gene, and computed gene expression indexes using the selected probes. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that probe selection improves gene expression estimates from exon arrays. The selected probes can be used in future analyses of other exon array datasets to compute gene expression indexes.
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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.