Protein network construction using reverse phase protein array data

Methods. 2017 Jul 15:124:89-99. doi: 10.1016/j.ymeth.2017.06.017. Epub 2017 Jun 24.

Abstract

In this paper, we introduce a novel computational method for constructing protein networks based on reverse phase protein array (RPPA) data to identify complex patterns in protein signaling. The method is applied to phosphoproteomic profiles of basal expression and activation/phosphorylation of 76 key signaling proteins in three breast cancer cell lines (MCF7, LCC1, and LCC9). Temporal RPPA data are acquired at 48h, 96h, and 144h after knocking down four genes in separate experiments. These genes are selected from a previous study as important determinants for breast cancer survival. Interaction networks are constructed by analyzing the expression levels of protein pairs using a multivariate analysis of variance model. A new scoring criterion is introduced to determine relevant protein pairs. Through a network topology based analysis, we search for wiring patterns to identify key proteins that are associated with significant changes in expression levels across various experimental conditions.

Keywords: Breast cancer; MANOVA; Network construction; RPPA; Topology analysis.

MeSH terms

  • ATPases Associated with Diverse Cellular Activities / antagonists & inhibitors
  • ATPases Associated with Diverse Cellular Activities / genetics
  • ATPases Associated with Diverse Cellular Activities / metabolism
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / metabolism
  • Breast Neoplasms / pathology
  • Cell Line, Tumor
  • Cysteine-Rich Protein 61 / antagonists & inhibitors
  • Cysteine-Rich Protein 61 / genetics
  • Cysteine-Rich Protein 61 / metabolism
  • Female
  • Gene Expression Regulation, Neoplastic*
  • Gene Regulatory Networks*
  • Humans
  • Intracellular Signaling Peptides and Proteins / antagonists & inhibitors
  • Intracellular Signaling Peptides and Proteins / genetics
  • Intracellular Signaling Peptides and Proteins / metabolism
  • MCF-7 Cells
  • Multivariate Analysis
  • Neoplasm Proteins / antagonists & inhibitors
  • Neoplasm Proteins / genetics*
  • Neoplasm Proteins / metabolism
  • Phosphorylation
  • Proteasome Endopeptidase Complex / genetics
  • Proteasome Endopeptidase Complex / metabolism
  • Protein Array Analysis / statistics & numerical data*
  • Protein Processing, Post-Translational*
  • RNA Polymerase II / antagonists & inhibitors
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism
  • Signal Transduction
  • Tumor Suppressor Proteins / antagonists & inhibitors
  • Tumor Suppressor Proteins / genetics
  • Tumor Suppressor Proteins / metabolism

Substances

  • CCN1 protein, human
  • Cysteine-Rich Protein 61
  • Intracellular Signaling Peptides and Proteins
  • Neoplasm Proteins
  • PSMC5 protein, human
  • RNA, Small Interfering
  • TOB1 protein, human
  • Tumor Suppressor Proteins
  • POLR2B protein, human
  • RNA Polymerase II
  • Proteasome Endopeptidase Complex
  • ATPases Associated with Diverse Cellular Activities