ArticleBMC genomics2004
Feature extraction and signal processing for nylon DNA microarrays.
Article in BMC genomics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fsh controls gene expression in fish both independently of and through steroid mediation.PloS one · 2013Pooled it
- Article
- Platelets alter gene expression profile in human brain endothelial cells in an in vitro model of cerebral malaria.PloS one · 2011Article
- Olfactory stem cells, a new cellular model for studying molecular mechanisms underlying familial dysautonomia.PloS one · 2010Article
- Gene expression signature-based screening identifies new broadly effective influenza a antivirals.PloS one · 2010Article
- Gene expression profiles characterize inflammation stages in the acute lung injury in mice.PloS one · 2010Article
- Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis.BMC genomics · 2009Article
- The adult boar testicular and epididymal transcriptomes.BMC genomics · 2009Article
- Early development of Moniliophthora perniciosa basidiomata and developmentally regulated genes.BMC microbiology · 2009Article
- A candidate molecular signature associated with tamoxifen failure in primary breast cancer.Breast cancer research : BCR · 2008Article
- Longitudinal analysis of gene expression in porcine skeletal muscle after post-injection local injury.Pharmaceutical research · 2007Article
- Article
- MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies.BMC genomics · 2006Article
- Gene expression patterns in rainbow trout, Oncorhynchus mykiss, exposed to a suite of model toxicants.Aquatic toxicology (Amsterdam, Netherlands) · 2006Article
- Gene expression profiling identifies molecular subgroups among nodal peripheral T-cell lymphomas.Oncogene · 2006Article
- Application of microarray technology in pulmonary diseases.Respiratory research · 2004Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-density DNA microarrays require automatic feature extraction methodologies and softwares. These can be a potential source of non-reproducibility of gene expression measurements. Variation in feature location or in signal integration methodology may be a significant contribution to the observed variance in gene expression levels.
resultsWe explore sources of variability in feature extraction from DNA microarrays on Nylon membrane with radioactive detection. We introduce a mathematical model of the signal emission and derive methods for correcting biases such as overshining, saturation or variation in probe amount. We also provide a quality metric which can be used qualitatively to flag weak or untrusted signals or quantitatively to modulate the weight of each experiment or gene in higher level analyses (clustering or discriminant analysis).
conclusionsOur novel feature extraction methodology, based on a mathematical model of the radioactive emission, reduces variability due to saturation, neighbourhood effects and variable probe amount. Furthermore, we provide a fully automatic feature extraction software, BZScan, which implements the algorithms described in this paper.
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.