title: Reconstruction of Protein Networks Using Reverse-Phase Protein Array Data.
abstract: In this chapter, we describe an approach to reconstruct cellular signaling networks based on measurements of protein activation after different stimulation experiments. As experimental platform reverse-phase protein arrays (RPPA) are used. RPPA allow the measurement of proteins and phosphoproteins across many samples in parallel with minimal sample consumption using a panel of highly target protein-specific antibodies. Functional interactions of proteins are modeled using a Boolean network. We describe the Boolean network reconstruction approach ddepn (dynamic deterministic effects propagation networks), which uses time course data to derive protein interactions based on perturbation experiments. We explain how the method works, give a practical application example, and describe how the results can be interpreted. Furthermore prior knowledge on signaling pathways is essential for network reconstruction. Here we describe the use of our software rBiopaxParser to integrate prior knowledge on protein signaling available in public databases. All applied methods are freely available as open-source R software packages. We describe the preparation of RPPA data as well as all relevant programming steps to format the RPPA data, to infer the prior knowledge, and to reconstruct and analyze the protein signaling networks.
authors.affiliation: Department of Medical Statistics, University Medical Center Göttingen, Göttingen, Germany. v.d.heyde@indivutest.com.|IndivuTest GmbH, Falkenried 88, 20251, Hamburg, Germany. v.d.heyde@indivutest.com.
authors.forename: Silvia
authors.initials: S
authors.lastname: von der Heyde
authors.affiliation: Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Johanna
authors.initials: J
authors.lastname: Sonntag
authors.affiliation: Department of Medical Statistics, University Medical Center Göttingen, Göttingen, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Kramer
authors.affiliation: TRON-Translational Oncology at the University Medical Center Mainz, Mainz, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Bender
authors.affiliation: Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Korf
authors.affiliation: Department of Medical Statistics, University Medical Center Göttingen, Göttingen, Germany.
authors.forename: Tim
authors.initials: T
authors.lastname: Beißbarth
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D006801:Humans; D040081:Protein Array Analysis / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D015398:Signal Transduction
keywords: Boolean mode ling; DDEPN; Network reconstruction; Protein signaling; Proteomics; Reverse-phase protein arrays