CARMAweb: Comprehensive R- and Bioconductor-based Web Service for Microarray Data Analysis

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Jul 18

PMID 16845058

Citations 122

Authors

Johannes Rainer

Fatima Sanchez-Cabo

Gernot Stocker

Alexander Sturn

Zlatko Trajanoski

Affiliations

Soon will be listed here.

Abstract

CARMAweb (Comprehensive R-based Microarray Analysis web service) is a web application designed for the analysis of microarray data. CARMAweb performs data preprocessing (background correction, quality control and normalization), detection of differentially expressed genes, cluster analysis, dimension reduction and visualization, classification, and Gene Ontology-term analysis. This web application accepts raw data from a variety of imaging software tools for the most widely used microarray platforms: Affymetrix GeneChips, spotted two-color microarrays and Applied Biosystems (ABI) microarrays. R and packages from the Bioconductor project are used as an analytical engine in combination with the R function Sweave, which allows automatic generation of analysis reports. These report files contain all R commands used to perform the analysis and guarantee therefore a maximum transparency and reproducibility for each analysis. The web application is implemented in Java based on the latest J2EE (Java 2 Enterprise Edition) software technology. CARMAweb is freely available at https://carmaweb.genome.tugraz.at.

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References

Brown M, Grundy W, Lin D, Cristianini N, Sugnet C, Furey T . Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A. 2000; 97(1):262-7. PMC: 26651. DOI: 10.1073/pnas.97.1.262. View

Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S . Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. PMC: 545600. DOI: 10.1186/gb-2004-5-10-r80. View

. Creating the gene ontology resource: design and implementation. Genome Res. 2001; 11(8):1425-33. PMC: 311077. DOI: 10.1101/gr.180801. View

Fellenberg K, Hauser N, Brors B, Neutzner A, Hoheisel J, Vingron M . Correspondence analysis applied to microarray data. Proc Natl Acad Sci U S A. 2001; 98(19):10781-6. PMC: 58552. DOI: 10.1073/pnas.181597298. View

Yeung K, Ruzzo W . Principal component analysis for clustering gene expression data. Bioinformatics. 2001; 17(9):763-74. DOI: 10.1093/bioinformatics/17.9.763. View

Sturn A, Quackenbush J, Trajanoski Z . Genesis: cluster analysis of microarray data. Bioinformatics. 2002; 18(1):207-8. DOI: 10.1093/bioinformatics/18.1.207. View

Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M . Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002; 18 Suppl 1:S96-104. DOI: 10.1093/bioinformatics/18.suppl_1.s96. View

Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N . ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003; 31(1):68-71. PMC: 165538. DOI: 10.1093/nar/gkg091. View

Bolstad B, Irizarry R, Astrand M, Speed T . A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003; 19(2):185-93. DOI: 10.1093/bioinformatics/19.2.185. View

10.

Schena M, Shalon D, Davis R, Brown P . Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995; 270(5235):467-70. DOI: 10.1126/science.270.5235.467. View

11.

Eisen M, Spellman P, Brown P, Botstein D . Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998; 95(25):14863-8. PMC: 24541. DOI: 10.1073/pnas.95.25.14863. View

12.

Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E . Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A. 1999; 96(6):2907-12. PMC: 15868. DOI: 10.1073/pnas.96.6.2907. View

13.

Tavazoie S, Hughes J, Campbell M, Cho R, Church G . Systematic determination of genetic network architecture. Nat Genet. 1999; 22(3):281-5. DOI: 10.1038/10343. View

14.

Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Wheeler D . GenBank. Nucleic Acids Res. 2004; 33(Database issue):D34-8. PMC: 540017. DOI: 10.1093/nar/gki063. View

15.

Psarros M, Heber S, Sick M, Thoppae G, Harshman K, Sick B . RACE: Remote Analysis Computation for gene Expression data. Nucleic Acids Res. 2005; 33(Web Server issue):W638-43. PMC: 1160250. DOI: 10.1093/nar/gki490. View

16.

Romualdi C, Vitulo N, Del Favero M, Lanfranchi G . MIDAW: a web tool for statistical analysis of microarray data. Nucleic Acids Res. 2005; 33(Web Server issue):W644-9. PMC: 1160257. DOI: 10.1093/nar/gki497. View

17.

Irizarry R, Bolstad B, Collin F, Cope L, Hobbs B, Speed T . Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003; 31(4):e15. PMC: 150247. DOI: 10.1093/nar/gng015. View

18.

Sturn A, Mlecnik B, Pieler R, Rainer J, Truskaller T, Trajanoski Z . Client-server environment for high-performance gene expression data analysis. Bioinformatics. 2003; 19(6):772-3. DOI: 10.1093/bioinformatics/btg074. View

19.

Smyth G, Yang Y, Speed T . Statistical issues in cDNA microarray data analysis. Methods Mol Biol. 2003; 224:111-36. DOI: 10.1385/1-59259-364-X:111. View

20.

Edwards D . Non-linear normalization and background correction in one-channel cDNA microarray studies. Bioinformatics. 2003; 19(7):825-33. DOI: 10.1093/bioinformatics/btg083. View