WebArrayDB: cross-platform microarray data analysis and public data repository
BioinformaticsPublished 14 July 2009Open access
Xiao-Qin Xia, Michael McClelland, Steffen Porwollik, Wenzhi Song, Xianling Cong, Yipeng Wang
Citations46
SJR quartileQ1
SJR score2.45
SNIP1.47
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
An open source integrated microarray database and analysis suite, WebArrayDB, has been developed that features convenient uploading of data for storage in a MIAME compliant fashion, and allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms.
Abstract
MOTIVATION: Cross-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. RESULTS: An 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.
Keywords
Computer ScienceBiochemistry, Genetics and Molecular Biology
Journal of the Royal Statistical Society Series B (Statistical Methodology)Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
108,736 Citations1995Yoav Benjamini, Yosef Hochberg
Genome biologyBioconductor: open software development for computational biology and bioinformatics
12,526 Citations2004Robert Gentleman, Vincent J. Carey +23 more
Details of the aims and methods of Bioconductor, the collaborative creation of extensible software for computational biology and bioinformatics, and current challenges are described.
Statistical Applications in Genetics and Molecular BiologyLinear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
12,048 Citations2004Gordon K. Smyth
BMC Research NotesIn silico prediction of protein-protein interactions in human macrophages
10,952 Citations2014Oussema Souiai, Fatma Z. Guerfali +3 more
This work integrated the PPI dataset from the Agile Protein Interaction DataAnalyzer with different meta-data to infer a contextualized macrophage-specific interactome using a combination of statistical methods and confirms that contextualizing interactomes improves the biological significance of bioinformatic analyses.
Proceedings of the National Academy of SciencesSignificance analysis of microarrays applied to the ionizing radiation response
10,671 Citations2001Virginia Goss Tusher, Robert Tibshirani +1 more
Statistics for biology and healthlimma: Linear Models for Microarray Data
5,869 Citations2005Gordon K. Smyth
This chapter starts with the simplest replicated designs and progresses through experiments with two or more groups, direct designs, factorial designs and time course experiments with technical as well as biological replication.
Bioinformaticsaffy—analysis of <i>Affymetrix GeneChip</i> data at the probe level
5,437 Citations2004Laurent Gautier, Leslie Cope +2 more
The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix that provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data.
Nature GeneticsMinimum information about a microarray experiment (MIAME)—toward standards for microarray data
4,106 Citations2001Alvis Brāzma, Pascal Hingamp +22 more
The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
Statistics in the health sciencesBioinformatics and Computational Biology Solutions Using R and Bioconductor
3,330 Citations2005Robert Gentleman
Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.
Computer applications in the biosciencesUse of within-array replicate spots for assessing differential expression in microarray experiments
1,421 Citations2005Gordon K. Smyth, Jean Michaud +1 more
A method is proposed for extracting more information from within-array replicate spots in microarray experiments by estimating the strength of the correlation between them that greatly improves the precision with which the genewise variances are estimated and thereby improves inference methods designed to identify differentially expressed genes.
Nature GeneticsFundamentals of experimental design for cDNA microarrays
1,059 Citations2002Gary A. Churchill
Fundamental issues of how to design an experiment to ensure that the resulting data are amenable to statistical analysis are discussed.
PubMedAnalysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer.
854 Citations2001John Welsh, Lisa M. Sapinoso +6 more
Primary prostate cancer was characterized by monitoring expression levels of more than 8900 genes in normal and malignant tissues, and a striking group of about 400 genes were identified that were overexpressed in tumor tissues.
Nucleic Acids ResearchArrayExpress--a public database of microarray experiments and gene expression profiles
770 Citations2006Helen Parkinson, Misha Kapushesky +14 more
The ArrayExpress Repository and Data Warehouse is a database of gene expression profiles selected from the repository and consistently re-annotated, which contains data from >50 000 hybridizations and >1 500000 individual expression profiles.
Genome biologyBioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data
460 Citations2002Lao H. Saal, Carl Troein +4 more
This work presents a web-based customizable bioinformatics solution called BioArray Software Environment (BASE) for the management and analysis of all areas of microarray experimentation.
Nature MethodsIndependence and reproducibility across microarray platforms
424 Citations2005Jennie Larkin, Bryan Frank +3 more
It is found that biological treatment had a far greater impact on measured expression than did platform for more than 90% of genes, a result validated by qRT-PCR, suggesting that sequence-specific effects may make expression predictions difficult to make using any technique.
BMC BioinformaticsCross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
233 Citations2005Patrick Warnat, Roland Eils +1 more
Cross-platform classification of multiple cancer microarray data sets yields discriminative gene expression signatures that are found and validated on a large number of microarray samples, generated by different laboratories and microarray technologies.
Trends in GeneticsComparison and meta-analysis of microarray data: from the bench to the computer desk
171 Citations2003Yves Moreau, Stein Aerts +3 more
This review focuses on the problems associated with the efficient access to and exchange of microarray data; the validation and comparison of data from different platforms (cDNA and short and long oligonucleotides); and the integrated statistical analysis of multiple data sets.
Nucleic Acids ResearchThe Stanford Microarray Database: implementation of new analysis tools and open source release of software
170 Citations2006János Demeter, Catherine C Beauheim +11 more
Several data analysis tools implemented in SMD are described and features of the software release are discussed, enabling other groups to create a local installation of SMD.
Genome biologyMatchMiner: a tool for batch navigation among gene and gene product identifiers
167 Citations2003Kimberly J. Bussey, David W. Kane +7 more
MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic' research.
BMC GenomicsPerformance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations
154 Citations2004Richard Shippy, Timothy J. Sendera +5 more
This study represents the most comprehensive and specifically designed comparison of short-oligonucleotide microarray platforms to date using the largest set of overlapping genes and provides guidelines for making cross-platform correlations.
Novartis Foundation symposiumOn Ontologies for Biologists: The Gene Ontology—Untangling the Web
134 Citations2002Michael Ashburner, Suzanna Lewis
The aim of the Gene Ontology (GO) Consortium is to provide a framework for both the description and the organisation of information concerning genes, and is presently concerned with three structured controlled vocabularies which can be used to describe three discrete biological domains.
Nucleic Acids ResearchExpression Profiler: next generation--an online platform for analysis of microarray data
124 Citations2004Misha Kapushesky, Patrick Kemmeren +9 more
The new architecture, Expression Profiler: next generation (EP:NG), modularizes the original design and allows individual analysis-task-related components to be developed by different groups and yet still seamlessly to work together and share the same user interface look and feel.
Nucleic Acids ResearchA primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase
121 Citations2004Martine Roovers
It is reported that the TrmI enzyme from the archaeon Pyrococcus abyssi is also a homotetramer, whereas the P.abyssi enzyme is region-specific and catalyses the formation of m(1)A at two adjacent positions in the T-loop of certain tRNAs.
Journal of Computational and Graphical StatisticsSimple Parallel Statistical Computing in R
116 Citations2007Anthony Rossini, Luke Tierney +1 more
This work presents a framework for the R statistical computing language that provides a simple yet powerful programming interface to a computational cluster of CPUs that allows the rapid development of R functions that distribute independent computations across the nodes of the computational cluster.
The FASEB JournalMolecular profiling of human prostate tissues: insights into gene expression patterns of prostate development during puberty
114 Citations2004Saravana M. Dhanasekaran, Atreya Dash +8 more
BMC BioinformaticsThe Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)
96 Citations2003Patrick J. Killion, Gavin Sherlock +1 more
The development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data.
BMC BioinformaticsWebArray: an online platform for microarray data analysis
75 Citations2005Xiao-Qin Xia, Michael McClelland +1 more
This work developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments, and provides a user-friendly interface for accessing a wide range of key functions of limma and others.
Nucleic Acids ResearchGEPAS, a web-based tool for microarray data analysis and interpretation
71 Citations2008Joaquín Tárraga, Ignacio Medina +12 more
An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers.
BMC BioinformaticsCross platform microarray analysis for robust identification of differentially expressed genes
71 Citations2007Roberta Bosotti, Giuseppe Locatelli +6 more
The high rate of confirmation found for both common and platform-specific genes suggests that the combination of platforms may overcome biases related to probe design and technical features, thereby accelerating the identification of trustworthy differentially expressed genes.
GenomicsAn integrated cross-platform prognosis study on neuroblastoma patients
58 Citations2008Qingrong Chen, Young Song +5 more
This study showed that gene expression studies performed in different platforms could be integrated for prognosis analysis after removing variation resulting from different platforms.
BioinformaticsNormalization of single-channel DNA array data by principal component analysis
24 Citations2004Radka Stoyanova, Troy D. Querec +2 more
A simple, robust and accurate procedure for the global normalization of datasets generated with single-channel DNA arrays based on principal component analysis, which makes minimal assumptions about the data and performs well in cases where other standard procedures produced biased estimates.
BioinformaticsIntegrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data
15 Citations2006Fei Pan, Kiran Kamath +11 more
The Integrative Array Analyzer is a comprehensive analysis and visualization software toolkit, which aims to facilitate the reuse of the large amount of cross-platform and cross-species microarray data.
Methods in enzymology on CD-ROM/Methods in enzymology[7] An Introduction to BioArray Software Environment
13 Citations2006Carl Troein, Johan Vallon‐Christersson +1 more
This introduction to BASE describes the basics of working with the software, both in general and in more detail for the various parts, and provides some hints about more advanced usage and a section on what is needed to set up your own BASE server.