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Explore Protein–Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal

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Protein-Protein Interaction Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2074))

Abstract

Protein–protein interactions (PPIs) control all functions and physiological states of the cell. Identification and understanding of novel PPIs would facilitate the discovery of new biological models and therapeutic targets for clinical intervention. Numerous resources and PPI databases have been developed to define a global interactome through the PPI data mining, curation, and integration of different types of experimental evidence obtained with various methods in different model systems. On the other hand, the recent advances in cancer genomics and proteomics have revealed a critical role of genomic alterations in acquisition of cancer hallmarks through a dysregulated network of oncogenic PPIs. Deciphering of cancer-specific interactome would uncover new mechanisms of oncogenic signaling for therapeutic interrogation. Toward this goal our team has developed a high-throughput screening platform to detect PPIs between cancer-associated proteins in the context of cancer cells. The established network of oncogenic PPIs, termed the OncoPPi network, is available through the OncoPPi Portal, an interactive web resource that allows to access and interpret a high-quality cancer-focused network of PPIs experimentally detected in cancer cell lines integrated with the analysis of mutual exclusivity of genomic alterations, cellular co-localization of interacting proteins, domain-domain interactions, and therapeutic connectivity. This chapter presents a guide to explore the OncoPPi network using the OncoPPi Portal to facilitate cancer biology.

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Acknowledgments

The results published here are in part based upon data generated by TCGA Research Network: http://cancergenome.nih.gov. This research was supported in part by the National Cancer Institute of the NIH (Cancer Target Discovery and Development Network grants U01CA168449 and U01CA217875), Emory University Research Committee grant, Winship Cancer Institute (NIH 5P30CA138292), and Fadlo R. Khuri Translational Research Award of the Winship Cancer Institute, Emory University.

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Authors and Affiliations

  1. Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA

    Andrey A. Ivanov

  2. Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA

    Andrey A. Ivanov

  3. Winship Cancer Institute, Emory University, Atlanta, GA, USA

    Andrey A. Ivanov

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  1. Andrey A. Ivanov
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Correspondence to Andrey A. Ivanov .

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Editors and Affiliations

  1. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Stefan Canzar

  2. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Francisca Rojas Ringeling

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Ivanov, A.A. (2020). Explore Protein–Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal. In: Canzar, S., Ringeling, F. (eds) Protein-Protein Interaction Networks. Methods in Molecular Biology, vol 2074. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9873-9_12

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  • DOI: https://doi.org/10.1007/978-1-4939-9873-9_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9872-2

  • Online ISBN: 978-1-4939-9873-9

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