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Identification of Differentially Expressed Genes

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Process Design for Natural Scientists

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 500))

Abstract

With the jABC it is possible to realize workflows for numerous questions in different fields. The goal of this project was to create a workflow for the identification of differentially expressed genes. This is of special interest in biology, for it gives the opportunity to get a better insight in cellular changes due to exogenous stress, diseases and so on. With the knowledge that can be derived from the differentially expressed genes in diseased tissues, it becomes possible to find new targets for treatment.

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References

  1. Blaese, L.: Data Mining for Unidentified Protein Sequences. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 73–87. Springer, Heidelberg (2014)

    Google Scholar 

  2. Ebert, B.E., Lamprecht, A.-L., Steffen, B., Blank, L.M.: Flux-P: Automating Metabolic Flux Analysis. Metabolites 2(4), 872–890 (2012)

    Article  Google Scholar 

  3. Lamprecht, A.-L. (ed.): User-Level Workflow Design - A Bioinformatics Perspective. LNCS, vol. 8311. Springer, Heidelberg (2013)

    Google Scholar 

  4. Lamprecht, A.-L., Margaria, T.: Scientific Workflows and XMDD. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 1–13. Springer, Heidelberg (2014)

    Google Scholar 

  5. Lamprecht, A.-L., Margaria, T., Steffen, B.: Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI. In: Măndoiu, I., Wang, S.-L., Zelikovsky, A. (eds.) ISBRA 2008. LNCS (LNBI), vol. 4983, pp. 445–456. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  6. Lamprecht, A.-L., Margaria, T., Steffen, B.: Bio-jETI: a framework for semantics-based service composition. BMC Bioinformatics 10(suppl. 10), S8 (2009)

    Google Scholar 

  7. Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., Giegerich, R.: GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics 9(suppl. 4), S13 (2008)

    Google Scholar 

  8. Lamprecht, A.-L., Naujokat, S., Margaria, T., Steffen, B.: Semantics-based composition of EMBOSS services. Journal of Biomedical Semantics 2(suppl. 1), S5 (2011)

    Google Scholar 

  9. Lamprecht, A.-L., Wickert, A.: The Course’s SIB Libraries. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 30–44. Springer, Heidelberg (2014)

    Google Scholar 

  10. Lis, M.: Constructing a Phylogenetic Tree. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 101–109. Springer, Heidelberg (2014)

    Google Scholar 

  11. Margaria, T., Steffen, B.: Agile IT: Thinking in User-Centric Models. In: Margaria, T., Steffen, B. (eds.) ISoLA 2008. CCIS, vol. 17, pp. 490–502. Springer, Heidelberg (2009)

    Google Scholar 

  12. Margaria, T., Steffen, B.: Business Process Modelling in the jABC: The One-Thing-Approach. In: Cardoso, J., van der Aalst, W. (eds.) Handbook of Research on Business Process Modeling. IGI Global (2009)

    Google Scholar 

  13. Margaria, T., Steffen, B.: Continuous Model-Driven Engineering. IEEE Computer 42(10), 106–109 (2009)

    Article  Google Scholar 

  14. Margaria, T., Steffen, B.: Simplicity as a Driver for Agile Innovation. Computer 43(6), 90–92 (2010)

    Article  Google Scholar 

  15. Margaria, T., Steffen, B.: Service-Orientation: Conquering Complexity with XMDD. In: Hinchey, M., Coyle, L. (eds.) Conquering Complexity, pp. 217–236. Springer, London (2012)

    Chapter  Google Scholar 

  16. Margaria, T., Steffen, B., Reitenspieß, M.: Service-Oriented Design: The Roots. In: Benatallah, B., Casati, F., Traverso, P. (eds.) ICSOC 2005. LNCS, vol. 3826, pp. 450–464. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  17. Naujokat, S., Lamprecht, A.-L., Steffen, B.: Loose programming with PROPHETS. In: de Lara, J., Zisman, A. (eds.) FASE 2012. LNCS, vol. 7212, pp. 94–98. Springer, Heidelberg (2012)

    Google Scholar 

  18. Rasch, B., Friese, M., Hofmann, W., Naumann, E.: Quantitative Methoden. Einführung in die Statistik für Psychologen und Sozialwissenschaftler, vol. 1. Springer (2009)

    Google Scholar 

  19. Reso, J.: Protein Classification Workflow. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 65–72. Springer, Heidelberg (2014)

    Google Scholar 

  20. Schulze, G.: Workflow for Rapid Metagenome Analysis. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 88–100. Springer, Heidelberg (2014)

    Google Scholar 

  21. Steffen, B., Margaria, T., Nagel, R., Jörges, S., Kubczak, C.: Model-Driven Development with the jABC. In: Bin, E., Ziv, A., Ur, S. (eds.) HVC 2006. LNCS, vol. 4383, pp. 92–108. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  22. Stranger, B.E., Forrest, M.S., Clark, A.G.: Genome-wide associations of gene expression variation in humans. PLoS Genetics 1, 695–704 (2005)

    Article  Google Scholar 

  23. Strothmann, K.: Gen-Chips–eine Einführung in die Technologie der moderenen Genexpressionsanalyse. Pharm Unserer Zeit 29(5), 303–308 (2000)

    Article  Google Scholar 

  24. Venables, W.N., Smith, D.M.: An Introduction to R. R Core Team (2012)

    Google Scholar 

  25. Vierheller, J.: Exploratory Data Analysis. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 110–126. Springer, Heidelberg (2014)

    Google Scholar 

  26. Zhijin, W., Irizarry, R.A.: Preprocessing of oligonucleotide array data. Nature Biotechnology 22, 656–658 (2004)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Potsdam University, Potsdam, D-14482, Germany

    Christine Schütt

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  1. Christine Schütt
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Editor information

Editors and Affiliations

  1. Chair Service and Software Engineering, Institute of Computer Science, University of Potsdam, Potsdam, Germany

    Anna-Lena Lamprecht

  2. Chair Software Engineering, Computer Science and Information Systems Department, University of Limerick and Lero, The Irish Software Research Center, Limerick, Ireland

    Tiziana Margaria

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Schütt, C. (2014). Identification of Differentially Expressed Genes. In: Lamprecht, AL., Margaria, T. (eds) Process Design for Natural Scientists. Communications in Computer and Information Science, vol 500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-45006-2_10

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  • DOI: https://doi.org/10.1007/978-3-662-45006-2_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-45005-5

  • Online ISBN: 978-3-662-45006-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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