Title:OPMSP: A Computational Method Integrating Protein Interaction and Sequence Information for the Identification of Novel Putative Oncogenes
Volume: 23
Issue: 12
Author(s): Lei Chen, Baoman Wang, ShaoPeng Wang, Jing Yang, Jerry Hu, ZhiQun Xie, Yuwei Wang, Tao Huang and Yu-Dong Cai
Affiliation:
Keywords:
Oncogene, protein-protein interaction, protein sequence, BLAST, shortest path algorithm.
Abstract: Oncogenes are genes that have the potential to cause cancer. Oncogene
research can provide insight into the occurrence and development of cancer,
thereby helping to prevent cancer and to design effective treatments. This study
proposes a network method called the oncogene prediction method based on
shortest path algorithm (OPMSP) for the identification of novel oncogenes in a
large protein network built using protein-protein interaction data. Novel putative
genes were extracted from the shortest paths connecting any two known oncogenes.
Then, they were filtered by a randomization test, and the linkages among
them and known oncogenes were measured by protein interaction and sequence
data. Thirty-seven new putative oncogenes were identified by this method. The
enrichment analysis of the 37 putative oncogenes indicated that they are highly associated with several
biological processes related to the initiation, progression and metastasis of tumors. Six of these
genes—ESR1, CDK9, SEPT2, HOXA10, LMX1B, and NR2C2—are extensively discussed. Several
lines of evidence indicate that they may be novel oncogenes.
