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Functional Characterization of Human Genes from Exon Expression and RNA Interference Results

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Book cover Bioinformatics and Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 910))

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Abstract

Complex biological systems comprise a large number of interacting molecules. The identification and detailed characterization of the functions of the involved genes and proteins are crucial for modeling and understanding such systems. To interrogate the various cellular processes, high-throughput techniques such as the Affymetrix Exon Array or RNA interference (RNAi) screens are powerful experimental approaches for functional genomics. However, they typically yield long gene lists that require computational methods to further analyze and functionally annotate the experimental results and to gain more insight into important molecular interactions. Here, we focus on bioinformatics software tools for the functional interpretation of exon expression data to discover alternative splicing events and their impact on gene and protein architecture, molecular networks, and pathways. We additionally demonstrate how to explore large lists of candidate genes as they also result from RNAi screens. In particular, our exemplary application studies show how to analyze the function of human genes that play a major role in human stem cells or viral infections.

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Acknowledgements

Part of this study was financially supported by the German National Genome Research Network (NGFN) and by the German Research Foundation (DFG), contract number KFO 129/1-2. The work was also conducted in the context of the DFG-funded Cluster of Excellence for Multimodal Computing and Interaction.

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Authors and Affiliations

  1. Max Planck Institute for Informatics, Saarbrücken, Germany

    Dorothea Emig, Hagen Blankenburg, Fidel Ramírez & Mario Albrecht

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  1. Dorothea Emig
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  2. Hagen Blankenburg
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  3. Fidel Ramírez
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  4. Mario Albrecht
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Correspondence to Mario Albrecht .

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Editors and Affiliations

  1. , Department of Pathology, The University of New Mexico, Camino de Salud 915, Albuquerque, 87131, New Mexico, USA

    Richard S. Larson

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Emig, D., Blankenburg, H., Ramírez, F., Albrecht, M. (2012). Functional Characterization of Human Genes from Exon Expression and RNA Interference Results. In: Larson, R. (eds) Bioinformatics and Drug Discovery. Methods in Molecular Biology, vol 910. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-965-5_3

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  • DOI: https://doi.org/10.1007/978-1-61779-965-5_3

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-964-8

  • Online ISBN: 978-1-61779-965-5

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