Mapping of TP53 protein network using Cytoscape software

Abstract

TP53 acts as a tumor suppressor in cancer. It induces cell cycle arrest or apoptosis in response to cellular
stress and damage. p53 gene alteration could cause uncontrolled cell proliferation. In the present study, we
used TP53 gene as the seed in the construction of a protein-protein interaction network to identify genes
that might involve in tumorgenesis process with TP53. TP53 protein interaction database was obtained
from STRING version 9.1 program. High-throughput experimental data, literature data and hypothetical
studies have been used to determine the roles of candidate genes in TP53 pathway. A total 500 genes from
STRING database loaded into Cytoscape version 2.8.3. The 1762 protein interactions were assembled and
visualized in y organic form. We found eight specific non-overlapping clusters of various sizes, which
emerged from the huge network of protein-interactors using MCODE version 1.32 clustering algorithm.
Biological Networks Gene Ontology (BiNGO) was used to determine two ontologies (molecular function and
biological process) involved in the protein network. Most of the genes mainly participated in gene and
protein expression, cell signaling and metabolism. A better understanding of the relationship between the
genes could aid in developing prognostic markers and better therapeutic strategies in cancer treatment.