Time-course network analysis reveals TNF-α can promote G1/S transition of cell cycle in vascular endothelial cells

Bioinformatics

Volumn 28, Issue 1, 2012, Pages 1-4

  Chen, Yang ^a   Gu, Jin ^a   Li, Dan ^a   Li, Shao ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CCND1 PROTEIN, HUMAN; CDKN1A PROTEIN, HUMAN; CELL CYCLE PROTEIN; CYCLIN D1; CYCLIN DEPENDENT KINASE INHIBITOR 1A; CYCLIN DEPENDENT KINASE INHIBITOR 1B; TUMOR NECROSIS FACTOR ALPHA; VASCULOTROPIN A;

ARTICLE; CELL CULTURE; CELL CYCLE; CELL DIVISION; CYTOLOGY; ENDOTHELIUM CELL; HUMAN; METABOLISM; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; UMBILICAL VEIN ENDOTHELIAL CELL;

CELL CYCLE; CELL CYCLE PROTEINS; CELL DIVISION; CELLS, CULTURED; CYCLIN D1; CYCLIN-DEPENDENT KINASE INHIBITOR P21; CYCLIN-DEPENDENT KINASE INHIBITOR P27; ENDOTHELIAL CELLS; HUMAN UMBILICAL VEIN ENDOTHELIAL CELLS; HUMANS; PROTEIN BINDING; PROTEIN INTERACTION MAPS; TUMOR NECROSIS FACTOR-ALPHA; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 84855178150     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr619     Document Type: Note

References (27)

1. Assenov, Y. et al. (2008) Computing topological parameters of biological networks. Bioinformatics, 24, 282-284.
2. Augustin, H.G. et al. (2009) Control of vascular morphogenesis and homeostasis through the angiopoietin-Tie system. Nat. Rev. Mol. Cell Biol., 10, 165-177.
3. Barabasi, A.L. et al. (2011) Network medicine: a network-based approach to human disease. Nat. Rev. Genet., 12, 56-68.
4. Bradley, J.R. (2008) TNF-mediated inflammatory disease. J. Pathol., 214, 149-160.
5. Dejana, E. (2004) Endothelial cell-cell junctions: happy together. Nat. Rev. Mol. Cell Biol., 5, 261-270.
6. Dennis, G. Jr et al. (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol., 4, P3.
7. Dormond, O. et al. (2002) Modulation of cdk2, cyclin D1, p16INK4a, p21WAF and p27Kip1 expression in endothelial cells by TNF/IFN gamma. Anticancer Res., 22, 3159-3163.
8. Fajardo, L.F. et al. (1992) Dual role of tumor necrosis factor-alpha in angiogenesis. Am. J. Pathol., 140, 539-544.
9. Frater-Schroder, M. et al. (1987) Tumor necrosis factor type alpha, a potent inhibitor of endothelial cell growth in vitro, is angiogenic in vivo. Proc. Natl Acad. Sci. USA, 84, 5277-5281.
10. Gu, J. et al. (2010) Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. BMC Syst. Biol., 4, 47.
11. Han, J.D. (2008) Understanding biological functions through molecular networks. Cell Res., 18, 224-237.
12. Huang, Y. and Li, S. (2010) Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network. BMC Bioinformatics, 11 (Suppl. 1), S32.
13. Keshava Prasad, T.S. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res., 37, D767-D772.
14. Krasinski, K. et al. (2001) In vivo blockade of tumor necrosis factor-alpha accelerates functional endothelial recovery after balloon angioplasty. Circulation, 104, 1754-1756.
15. Li, C. and Wong, W.H. (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl Acad. Sci. USA, 98, 31-36.
16. Li, S. et al. (2011) Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC Syst. Biol., 5 (Suppl. 1), S10.
17. Lindner, H. et al. (1997) Peripheral blood mononuclear cells induce programmed cell death in human endothelial cells and may prevent repair: role of cytokines. Blood, 89, 1931-1938.
18. Liu, W.C. et al. (2007)Anetwork perspective on the topological importance of enzymes and their phylogenetic conservation. BMC Bioinformatics, 8, 121.
19. Mantovani, A. and Sica, A. (2010) Macrophages, innate immunity and cancer: balance, tolerance, and diversity. Curr. Opin. Immunol., 22, 231-237.
20. Peri, S. et al. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res., 13, 2363-2371.
21. Stark, C. et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res., 34, D535-D539.
22. Wada, Y. et al. (2009) A wave of nascent transcription on activated human genes. Proc. Natl Acad. Sci. USA, 106, 18357-18361.
23. Wojciak-Stothard, B. et al. (1998) Regulation of TNF-alpha-induced reorganization of the actin cytoskeleton and cell-cell junctions by Rho, Rac, and Cdc42 in human endothelial cells. J. Cell Physiol., 176, 150-165.
24. Wu, X. et al. (2008) Network-based global inference of human disease genes. Mol. Syst. Biol., 4, 189.
25. Yan, H. et al. (2010) A formal model for analyzing drug combination effects and its application in TNF-alpha-induced NFkappaB pathway. BMC Syst. Biol., 4, 50.
26. Zhang, H. et al. (2009) Role of TNF-alpha in vascular dysfunction. Clin. Sci., 116, 219-230.
27. Zhao, S. and Li, S. (2010) Network-based relating pharmacological and genomic spaces for drug target identification. PLoS One, 5, e11764.