Protein network construction using reverse phase protein array data

Rency S. Varghese, Yiming Zuo, Yi Zhao, Yong Wei Zhang, Sandra A. Jablonski, Mariaelena Pierobon, Emanuel F. Petricoin, Habtom W. Ressom*, Louis M. Weiner

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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 48 h, 96 h, and 144 h 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.

Original languageEnglish
Pages (from-to)89-99
Number of pages11
StatePublished - 15 Jul 2017
Externally publishedYes


  • Breast cancer
  • Network construction
  • RPPA
  • Topology analysis


Dive into the research topics of 'Protein network construction using reverse phase protein array data'. Together they form a unique fingerprint.

Cite this