Abstract
Current projects in Systems Biology often produce a multitude of different high-throughput data sets that need to be managed, processed, and analyzed in an integrated fashion. In this paper, we present the OmixAnalyzer, a web-based tool for management and analysis of heterogeneous omics data sets. It currently supports gene microarrays, miRNAs, and exon-arrays; support for mass spectrometry-based proteomics is on the way, and further types can easily be added due to its plug-and-play architecture. Distinct from competitor systems, the OmixAnalyzer supports management, analysis, and visualization of data sets; it features a mature system of access rights, handles heterogeneous data sets including metadata, supports various import and export formats, includes pipelines for performing all steps of data analysis from normalization and quality control to differential analysis, clustering and functional enrichment, and it is capable of producing high quality figures and reports. The system builds only on open source software and is available on request as sources or as a ready-to-run software image. An instance of the tool is available for testing at omixanalyzer.informatik.hu-berlin.de.
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References
Baranzini, S.E., Mudge, J., van Velkinburgh, J.C., Khankhanian, P., Khrebtukova, I., et al.: Genome, epigenome and rna sequences of monozygotic twins discordant for multiple sclerosis. Nature 464(7293), 1351–1356 (2010)
Battke, F., Symons, S., Nieselt, K.: Mayday – integrative analysis for expression data. BMC Bioinformatics 11, 121 (2011)
Birney, E., Hudson, T.J., Green, E.D., Gunter, C., Eddy, S., et al.: Prepublication data sharing. Nature 461(7261), 168–170 (2009)
Dreher, F., Kreitler, T., Hardt, C., Kamburov, A., Yildirimman, R., et al.: Dipsbc-data integration platform for systems biology collaborations. BMC Bioinformatics 13(1), 85 (2012)
Goecks, J., Nekrutenko, A., Taylor, J.: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11(8), R86 (2010)
Joosten, M., Seitz, V., Zimmermann, K., Sommerfeld, A., Berg, E., et al.: Histone acetylation and dna demethylation of t-cells result in an anaplastic large cell lymphoma-like phenotype. Haematologica 98(2), 247–254 (2013)
Kallio, M.A., Tuimala, J.T., Hupponen, T., Klemela, P., Gentile, M., et al.: Chipster: user-friendly analysis software for microarray and other high-throughput data. BMC Genomics 12, 507 (2011)
Koschmieder, A., Zimmermann, K., Trissl, S., Stoltmann, T., Leser, U.: Tools for managing and analyzing microarray data. Brief. in Bioinf. 13, 46–60 (2012)
Medina, I., Carbonell, J., Pulido, L., Madeira, S., Goetz, S., et al.: Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucl. Acids Res. 38(suppl.) W210–W213 (2010)
Paton, N.W.: Managing and sharing experimental data: standards, tools and pitfalls. Biochem. Soc. Trans. 36(Pt. 1), 33–36 (2008)
Rohn, H., Junker, A., Hartmann, A., Grafahrend-Belau, E., Treutler, H., et al.: Vanted v2: a framework for systems biology applications. BMC Syst. Biol. 6(1), 139 (2012)
Schadt, E.E., Linderman, M.D., Sorenson, J., Lee, L., Nolan, G.P.: Computational solutions to large-scale data management and analysis. Nat. Rev. Genet. 11(9), 647–657 (2010)
Seitz, V., Thomas, P., Zimmermann, K., Paul, U., Ehlers, A., et al.: Classical hodgkin’s lymphoma shows epigenetic features of abortive plasma cell differentiation. Haematologica 96(6), 863–870 (2011)
Smith, R.N., Aleksic, J., Butano, D., Carr, A., Contrino, S., et al.: Intermine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data 28(23), 3163–3165 (2012)
Wolstencroft, K., Owen, S., du Preez, F., Krebs, O., Mueller, W., et al.: The seek: a platform for sharing data and models in systems biology. Methods in Enzymology 500, 629 (2011)
Wruck, W., Peuker, M., Regenbrecht, C.R.: Data management strategies for multinational large-scale systems biology projects. Brief. in Bioinf. (2012)
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Stoltmann, T., Zimmermann, K., Koschmieder, A., Leser, U. (2013). OmixAnalyzer – A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets. In: Baker, C.J.O., Butler, G., Jurisica, I. (eds) Data Integration in the Life Sciences. DILS 2013. Lecture Notes in Computer Science(), vol 7970. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39437-9_4
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DOI: https://doi.org/10.1007/978-3-642-39437-9_4
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