ArticleNucleic acids research2010
Estimating the proportion of microarray probes expressed in an RNA sample.
Article in Nucleic acids research, 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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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial.EBioMedicine · 2018Trial
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- Resistance training in young men induces muscle transcriptome-wide changes associated with muscle structure and metabolism refining the response to exercise-induced stress.European journal of applied physiology · 2018Article
- limma powers differential expression analyses for RNA-sequencing and microarray studies.Nucleic acids research · 2015Article
- Ragweed (Ambrosia artemisiifolia) pollen allergenicity: SuperSAGE transcriptomic analysis upon elevated CO2 and drought stress.BMC plant biology · 2014Article
- Absence/presence calling in microarray-based CGH experiments with non-model organisms.Nucleic acids research · 2014Article
- Photonic crystal enhancement of a homogeneous fluorescent assay using submicron fluid channels fabricated by E-jet patterning.Journal of biophotonics · 2014Article
- The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease.RNA (New York, N.Y.) · 2013Article
- Generalization of the normal-exponential model: exploration of a more accurate parametrisation for the signal distribution on Illumina BeadArrays.BMC bioinformatics · 2012Article
- BeadArray expression analysis using bioconductor.PLoS computational biology · 2011Article
- Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips.Nucleic acids research · 2010Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A fundamental question in microarray analysis is the estimation of the number of expressed probes in different RNA samples. Negative control probes available in the latest microarray platforms, such as Illumina whole genome expression BeadChips, provide a unique opportunity to estimate the number of expressed probes without setting a threshold. A novel algorithm was proposed in this study to estimate the number of expressed probes in an RNA sample by utilizing these negative controls to measure background noise. The performance of the algorithm was demonstrated by comparing different generations of Illumina BeadChips, comparing the set of probes targeting well-characterized RefSeq NM transcripts with other probes on the array and comparing pure samples with heterogenous samples. Furthermore, hematopoietic stem cells were found to have a larger transcriptome than progenitor cells. Aire knockout medullary thymic epithelial cells were shown to have significantly less expressed probes than matched wild-type cells.
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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.