Protein-protein interaction network

Analysis of protein-protein interaction network in chronic obstructive pulmonary disease

Y. P. Yuan, Shi, Y. H., and Gu, W. C., “Analysis of protein-protein interaction network in chronic obstructive pulmonary disease”, vol. 13, pp. 8862-8869, 2014.

Chronic obstructive pulmonary disease (COPD) is a growing cause of morbidity and mortality throughout the world. The purpose of our study was to uncover biomarkers and explore its pathogenic mechanisms at the molecular level. The gene expression profiles of COPD samples and normal controls were downloaded from Gene Expression Omnibus. Matlab was used for data preprocessing and SAM4.0 was applied to determine the differentially expressed genes (DEGs).

Protein-protein interaction network analysis of osteoarthritis-related differentially expressed genes

Y. C. Zhu, Deng, B. Y., Zhang, L. G., Xu, P., Du, X. P., Zhang, Q. G., and Yang, B., “Protein-protein interaction network analysis of osteoarthritis-related differentially expressed genes”, vol. 13, pp. 9343-9351, 2014.

The purpose of this study was to identify genes and pathways for osteoarthritis (OA) diagnosis and therapy. We downloaded the gene expression profile of OA from Gene Expression Omnibus (GEO) database including 10 early OA, 9 late OA, and 5 normal control samples. Next, we screened differentially expressed genes (DEGs) between early- and late-stage OA samples comparing with healthy control samples.

Analysis of differentially expressed genes in various stages of Duchenne muscular dystrophy by using a network view

D. Wang, Wang, Z. J., Song, X. X., Pu, L. H., Li, X., and Wang, Y., “Analysis of differentially expressed genes in various stages of Duchenne muscular dystrophy by using a network view”, vol. 12, pp. 4480-4488, 2013.

Duchenne muscular dystrophy (DMD), which is caused by mutations in the X-linked dystrophin gene, is a severe and progressive neuromuscular disease with no available cure. By integrating 2 microarray datasets from the Gene Expression Omnibus, we identified differentially expressed genes in 2 stages of DMD and systematically explored their potential disease-related mechanisms using a network view. Twenty differentially expressed genes were detected in various stages of DMD.

Protein-protein interaction network and significant gene analysis of osteoporosis

X. M. Wu, Ma, X., Tang, C., Xie, K. N., Liu, J., Guo, W., Yan, Y. L., Shen, G. H., and Luo, E. P., “Protein-protein interaction network and significant gene analysis of osteoporosis”, vol. 12, pp. 4751-4759, 2013.

This study used DNA microarray data to identify differentially expressed genes of osteoporosis and provide useful information for treatments of the disease. We downloaded gene expression data of Osteoporosis GSE35956 from the Gene Expression Omnibus database, which included five normal and five osteoporosis samples. We then identified the differentially expressed genes between normal and disease samples using the R language software, and constructed the protein interaction network. DAVID was used to perform the biological process enrichment and KEGG pathway cluster analyses.

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