Protein Interaction Network Construction and Biological Pathway Analysis Related to Atherosclerosis_Journal of Biomedical Engineering

Authors：

 LIQuhuan ¹ , GUShanshan ² , LINa ¹ , LIZhenyang ¹ , LAIWenlong ³ , ZENGYang ¹

1. Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Engineering, South China University of Technology, Guangzhou 510006, China;
2. Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China;
3. School of Medicine, Tsinghua University, Beijing 100084, China;

Corresponding author：

LIQuhuan, Email: liqh@scut.edu.cn

Keywords：

atherosclerosis; interaction network; Hub protein; biological pathway

DOI：

10.7507/1001-5515.20150223

Video：

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Atherosclerosis is a complex disease characterized by lipid accumulation in the vascular wall and influenced by multiple genetic and environmental factors. To understand the mechanisms of molecular regulation related to atherosclerosis better, a protein interaction network was constructed in the present study. Genes were collected in nucleotide database and interactions were downloaded from Biomolecular Object Network Database (BOND). The interactional data were imported into the software Cytoscape to construct the interaction network, and then the degree characteristics of the network were analyzed for Hub proteins. Statistical significance pathways and diseases were figured out by inputting Hub proteins to KOBAS2.0. The complete pathway network related to atherosclerosis was constructed. The results identified a series of key genes related to atherosclerosis, which would be the potential promising drug targets for effective prevention.

Citation： LIQuhuan, GUShanshan, LINa, LIZhenyang, LAIWenlong, ZENGYang. Protein Interaction Network Construction and Biological Pathway Analysis Related to Atherosclerosis. Journal of Biomedical Engineering, 2015, 32(6): 1255-1260. doi: 10.7507/1001-5515.20150223 Copy

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1. POULTER N, Global risk of cardiovascular disease, Heart[J].2003, 89(suppl 2):ii2-ii5.
2. CHYU K Y, SHAH P K. Emerging therapies for atherosclerosis prevention and management[J]. Cardiol Clin, 2011, 29(1):123-135.
3. FLÓREZ A F, PARK D, BHAK J, et al. Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection[J]. BMC Bioinformatics, 2010, 11(1):484.
4. ALFARANO C, ANDRADE C E, ANTHONY K, et al. The biomolecular interaction network database and related tools 2005 update[J]. Nucleic Acids Res, 2005, 33(Database issue):D418-D424.
5. SHANNON P, MARKIEL A, OZIER O, et al. Cytoscape:a software environment for integrated models of biomolecular interaction networks[J]. Genome Res, 2003, 13(11):2498-2504.
6. ASSENOV Y, RAMÍREZ F, SCHELHORN S E, et al. Computing topological parameters of biological networks[J]. Bioinformatics, 2008, 24(2):282-284.
7. WU Jianmin, MAO Xizeng, CAI Tao, et al. KOBAS server:a web-based platform for automated annotation and pathway identification[J]. Nucleic Acids Res, 2006, 34(suppl. 2):W720-W724.
8. DAVIES S S, ROBERTS L J. F2-isoprostanes as an indicator and risk factor for coronary heart disease[J]. Free Radic Biol Med, 2011, 50(5):559-566.
9. SHERVA R, FORD C E, ECKFELDT J H, et al. Pharmacogenetic effect of the stromelysin (MMP3) polymorphism on stroke risk in relation to antihypertensive treatment:the genetics of hypertension associated treatment study[J]. Stroke, 2011, 42(2):330-335.
10. SCHWARTZ R S, BORISSOFF J I, SPRONK H M, et al., The hemostatic system as a modulator of atherosclerosis, New Engl J Med[J].2011, 364(18):1746-1760.
11. WANG H, YIN Y, LI W, et al., Over-expression of PDGFR-beta promotes PDGF-induced proliferation, migration, and angiogenesis of EPCs through PI3K/Akt signaling pathway, PloS One[J].2012, 7(2):e30503.
12. FERRARA N, KERBEL R S, Angiogenesis as a therapeutic target, Nature[J].2005, 438(7070):967-974.
13. FREITAS W M, QUAGLIA L A, SANTOS S N, et al. Association of systemic inflammatory activity with coronary and carotid atherosclerosis in the very elderly[J]. Atherosclerosis, 2011, 216(1):212-216.
14. STOUT R, Diabetes and atherosclerosis, Biomed Pharmacother[J].1993, 47(1):1-2.
15. NASCIMENTO I S, QUAIO C R, SINICATO N A, et al. Aspects of atherosclerosis and metabolic syndrome in lupus erythematosus[J]. Acta Reumatol Port, 2010, 35(3):294-300.
16. HANSSON G K, HERMANSSON A. The immune system in atherosclerosis[J]. Nat Immunol, 2011, 12(3):204-212.

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