A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal

BMC Genomics

Marijana Radonjic¹  Chris T. Evelo⁴  Michiel E. Adriaens²  Thomas Kelder¹  Varshna S. Goelela³  Lars M.T. Eijssen⁴ 

[1] EdgeLeap B.V., Hooghiemstraplein 15, Utrecht, 3514 AX, The Netherlands;Department of Experimental Cardiology, Academic Medical Center, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands;Current address: Charles River Laboratories, BioFocus, Discovery Services, Darwinweg 24, Leiden, 2333 CR, The Netherlands;Department of Bioinformatics-BiGCaT, Maastricht University, Universiteitssingel 50, Maastricht, 6229 ER, The Netherlands

关键词: Quality control;    Normalization;    Data analysis;    Transcriptomics;    Illumina bead array;    Microarray;   

Others  :  1219265
DOI  :  10.1186/s12864-015-1689-8

 received in 2015-01-05, accepted in 2015-06-05,  发布年份 2015

【 摘 要 】

Background

Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows.

Results

To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis.

The module accepts data exported from Illumina’s GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools.

Conclusions

The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org. A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

【 授权许可】

   
2015 Eijssen et al.

【 图 表 】

Fig. 1.

【 参考文献 】

• [1]Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, Bennett H et al.. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res. 2004; 14(11):2347-56.
• [2]Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E et al.. ArrayExpress update-simplifying data submissions. Nucleic Acids Res. 2014.
• [3]Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M et al.. NCBI GEO: archive for functional genomics data sets–update. Nucleic Acids Res. 2013; 41(Database issue):D991-5.
• [4]Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD. illuminaio: An open source IDAT parsing tool for Illumina microarrays. F1000Research. 2013; 2:264.
• [5]Dunning MJ, Smith ML, Ritchie ME, Tavare S. beadarray: R classes and methods for Illumina bead-based data. Bioinformatics. 2007; 23(16):2183-4.
• [6]Du P, Kibbe WA, Lin SM. lumi: a pipeline for processing Illumina microarray. Bioinformatics. 2008; 24(13):1547-8.
• [7]Smyth GK. Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor. Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, editors. Springer, New York; 2005: p.397-420.
• [8]Eijssen LM, Jaillard M, Adriaens ME, Gaj S, de Groot PJ, Muller M et al.. User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. Nucleic acids research. 2013; 41(Web Server issue):W71-6.
• [9]Kallio MA, Tuimala JT, Hupponen T, Klemela P, Gentile M, Scheinin I et al.. Chipster: user-friendly analysis software for microarray and other high-throughput data. BMC Genomics. 2011; 12:507. BioMed Central Full Text
• [10]Lin K, Kools H, de Groot PJ, Gavai AK, Basnet RK, Cheng F et al.. MADMAX - Management and analysis database for multiple ~ omics experiments. J Integr Bioinform. 2011; 8(2):160.
• [11]Schultze JL, Eggle D. IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform. Bioinformatics. 2007; 23(11):1431-3.
• [12]Shi W, Oshlack A, Smyth GK. Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips. Nucleic Acids Res. 2010; 38(22):e204.
• [13]Du P, Kibbe WA, Lin SM. nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays. Biology direct. 2007; 2:16. BioMed Central Full Text
• [14]Ritchie ME, Dunning MJ, Smith ML, Shi W, Lynch AG. BeadArray expression analysis using bioconductor. PLoS Comput Biol. 2011; 7(12):e1002276.
• [15]van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR et al.. Presenting and exploring biological pathways with PathVisio. BMC bioinformatics. 2008; 9:399. BioMed Central Full Text