Identification of Lung-Cancer-Related Genes with the Shortest Path Approach in a Protein-Protein Interaction Network

Lung cancer is one of the leading causes of cancer mortality worldwide. The main types of lung cancer are small cell lung cancer (SCLC) and nonsmall cell lung cancer (NSCLC). In this work, a computational method was proposed for identifying lung-cancer-related genes with a shortest path approach in...

Full description

Saved in:

Bibliographic Details
Published in:	BioMed research international 2013-01, Vol.2013, p.267375-8
Main Authors:	Li, Bi-Qing, You, Jin, Chen, Lei, Zhang, Jian, Zhang, Ning, Li, Hai-Peng, Huang, Tao, Kong, Xiang-Yin, Cai, Yu-Dong
Format:	Article
Language:	eng
Subjects:	Apoptosis Biology Carcinoma, Non-Small-Cell Lung - genetics Cell cycle Gene expression Gene Expression Profiling - methods Gene Expression Regulation, Neoplastic Genes Genes, Neoplasm - genetics Genetic aspects Genetic Association Studies Humans Lung cancer Lung Neoplasms - genetics Medical research Physiological aspects Protein Interaction Maps - genetics Protein-protein interactions Proteins Risk factors Small Cell Lung Carcinoma - genetics
Online Access:	Request full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	Lung cancer is one of the leading causes of cancer mortality worldwide. The main types of lung cancer are small cell lung cancer (SCLC) and nonsmall cell lung cancer (NSCLC). In this work, a computational method was proposed for identifying lung-cancer-related genes with a shortest path approach in a protein-protein interaction (PPI) network. Based on the PPI data from STRING, a weighted PPI network was constructed. 54 NSCLC- and 84 SCLC-related genes were retrieved from associated KEGG pathways. Then the shortest paths between each pair of these 54 NSCLC genes and 84 SCLC genes were obtained with Dijkstra’s algorithm. Finally, all the genes on the shortest paths were extracted, and 25 and 38 shortest genes with a permutation P value less than 0.05 for NSCLC and SCLC were selected for further analysis. Some of the shortest path genes have been reported to be related to lung cancer. Intriguingly, the candidate genes we identified from the PPI network contained more cancer genes than those identified from the gene expression profiles. Furthermore, these genes possessed more functional similarity with the known cancer genes than those identified from the gene expression profiles. This study proved the efficiency of the proposed method and showed promising results.
ISSN:	2314-6133 2314-6141