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Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data

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Cancer Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1711))

Abstract

With the extraordinary rise in available biological data, biologists and clinicians need unbiased tools for data integration in order to reach accurate, succinct conclusions. Network biology provides one such method for high-throughput data integration, but comes with its own set of algorithmic problems and needed expertise. We provide a step-by-step guide for using Omics Integrator, a software package designed for the integration of transcriptomic, epigenomic, and proteomic data. Omics Integrator can be found at http://fraenkel.mit.edu/omicsintegrator.

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Acknowledgments

This work was supported by grants from National Institute of Health (R01-NS089076, T32-GM008334, and U01-CA184898). We thank Tobias Ehrenberger and Renan Escalante-Chong for helpful comments on the manuscript.

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Authors and Affiliations

  1. Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

    Amanda J. Kedaigle & Ernest Fraenkel

  2. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Ernest Fraenkel

Authors
  1. Amanda J. Kedaigle
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  2. Ernest Fraenkel
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Corresponding author

Correspondence to Ernest Fraenkel .

Editor information

Editors and Affiliations

  1. NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

    Louise von Stechow

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Kedaigle, A.J., Fraenkel, E. (2018). Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data. In: von Stechow, L. (eds) Cancer Systems Biology. Methods in Molecular Biology, vol 1711. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7493-1_2

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  • DOI: https://doi.org/10.1007/978-1-4939-7493-1_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7492-4

  • Online ISBN: 978-1-4939-7493-1

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