ArticleBioinformatics (Oxford, England)2009
WebArrayDB: cross-platform microarray data analysis and public data repository.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- Uniformly shaped harmonization combines human transcriptomic data from different platforms while retaining their biological properties and differential gene expression patterns.Frontiers in molecular biosciences · 2023Article
- Transcriptomic Harmonization as the Way for Suppressing Cross-Platform Bias and Batch Effect.Biomedicines · 2022Review
- MatchMixeR: a cross-platform normalization method for gene expression data integration.Bioinformatics (Oxford, England) · 2020Article
- Shambhala: a platform-agnostic data harmonizer for gene expression data.BMC bioinformatics · 2019Article
- Novel DNA Binding and Regulatory Activities for σJournal of bacteriology · 2017Article
- Article
- Novel Two-Step Hierarchical Screening of Mutant Pools Reveals Mutants under Selection in Chicks.Infection and immunity · 2016Article
- DNA microarray integromics analysis platform.BioData mining · 2015Article
- XMS: cross-platform normalization method for multimodal mass spectrometric tissue profiling.Journal of the American Society for Mass Spectrometry · 2015Article
- Identification of a Salmonella ancillary copper detoxification mechanism by a comparative analysis of the genome-wide transcriptional response to copper and zinc excess.Microbiology (Reading, England) · 2014Article
- Novel determinants of intestinal colonization of Salmonella enterica serotype typhimurium identified in bovine enteric infection.Infection and immunity · 2013Article
- Probing the ArcA regulon under aerobic/ROS conditions in Salmonella enterica serovar Typhimurium.BMC genomics · 2013Article
- Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ⁵⁴ (RpoN) regulon of Salmonella Typhimurium LT2.BMC genomics · 2013Article
- Mapping and regulation of genes within Salmonella pathogenicity island 12 that contribute to in vivo fitness of Salmonella enterica Serovar Typhimurium.Infection and immunity · 2013Article
- virtualArray: a R/bioconductor package to merge raw data from different microarray platforms.BMC bioinformatics · 2013Article
- Cross-platform microarray meta-analysis for the mouse jejunum selects novel reference genes with highly uniform levels of expression.PloS one · 2013Article
- Article
- Workflows for microarray data processing in the Kepler environment.BMC bioinformatics · 2012Article
- Gene expression analysis of Salmonella enterica Enteritidis Nal(R) and Salmonella enterica Kentucky 3795 exposed to HCl and acetic acid in rich medium.Foodborne pathogens and disease · 2012Article
- Evaluation of the role of functional constraints on the integrity of an ultraconserved region in the genus Drosophila.PLoS genetics · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationCross-platform microarray analysis is an increasingly important research tool, but researchers still lack open source tools for storing, integrating and analyzing large amounts of microarray data obtained from different array platforms.
resultsAn open source integrated microarray database and analysis suite, WebArrayDB (http://www.webarraydb.org), has been developed that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion, and allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters. AVAILABILITY: The software package is available for the use on a public web server (http://www.webarraydb.org) or can be downloaded. are available at Bioinformatics online.
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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.