WebArrayDB: Cross-platform Microarray Data Analysis and Public Data Repository

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2009 Jul 16

PMID 19602526

Citations 29

Authors

Xiao-Qin Xia

Michael McClelland

Steffen Porwollik

Wenzhi Song

Xianling Cong

Yipeng Wang

Affiliations

Soon will be listed here.

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.

Citing Articles

Uniformly shaped harmonization combines human transcriptomic data from different platforms while retaining their biological properties and differential gene expression patterns.

Borisov N, Tkachev V, Simonov A, Sorokin M, Kim E, Kuzmin D Front Mol Biosci. 2023; 10:1237129.

PMID: 37745690 PMC: 10511763. DOI: 10.3389/fmolb.2023.1237129.

Transcriptomic Harmonization as the Way for Suppressing Cross-Platform Bias and Batch Effect.

Borisov N, Buzdin A Biomedicines. 2022; 10(9).

PMID: 36140419 PMC: 9496268. DOI: 10.3390/biomedicines10092318.

MatchMixeR: a cross-platform normalization method for gene expression data integration.

Zhang S, Shao J, Yu D, Qiu X, Zhang J Bioinformatics. 2020; 36(8):2486-2491.

PMID: 31904810 PMC: 7868049. DOI: 10.1093/bioinformatics/btz974.

Shambhala: a platform-agnostic data harmonizer for gene expression data.

Borisov N, Shabalina I, Tkachev V, Sorokin M, Garazha A, Pulin A BMC Bioinformatics. 2019; 20(1):66.

PMID: 30727942 PMC: 6366102. DOI: 10.1186/s12859-019-2641-8.

Novel DNA Binding and Regulatory Activities for σ (RpoN) in Salmonella enterica Serovar Typhimurium 14028s.

Bono A, Hartman C, Solaimanpour S, Tong H, Porwollik S, McClelland M J Bacteriol. 2017; 199(12).

PMID: 28373272 PMC: 5446619. DOI: 10.1128/JB.00816-16.

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