Discovery approaches to UPR in athero-susceptible endothelium in vivo

Methods in Enzymology

Volumn 489, Issue C, 2011, Pages 109-126

  Civelek, Mete ^a,b,c   Manduchi, Elisabetta ^a   Grant, Gregory R ^a   Stoeckert Jr , Christian J ^a   Davies, Peter F ^a,b  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTERY ENDOTHELIUM; ARTICLE; ATHEROSCLEROSIS; CARDIOVASCULAR RISK; CONTROLLED STUDY; ENDOPLASMIC RETICULUM STRESS; ENZYME ANALYSIS; GENE EXPRESSION; IN VIVO STUDY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN EXPRESSION; QUALITY CONTROL; RNA EXTRACTION; UNFOLDED PROTEIN RESPONSE;

EID: 79251481854     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385116-1.00007-8     Document Type: Chapter

References (21)

1. S.E. Calvano, W. Xiao, D.R. Richards, R.M. Felciano, H.V. Baker, R.J. Cho, R.O. Chen, B.H. Brownstein, J.P. Cobb, S.K. Tschoeke, C. Miller-Graziano, and L.L. Moldawer A network-based analysis of systemic inflammation in humans Nature 437 2005 1032 1037
2. M. Civelek, E. Manduchi, R.J. Riley, C.J. Stoeckert Jr., and P.F. Davies Chronic endoplasmic reticulum stress activates unfolded protein response in arterial endothelium in regions of susceptibility to atherosclerosis Circ. Res. 105 2009 453 461
3. M.S. Cline, M. Smoot, E. Cerami, A. Kuchinsky, N. Landys, C. Workman, R. Christmas, I. Avila-Campilo, M. Creech, B. Gross, K. Hanspers, and R. Isserlin Integration of biological networks and gene expression data using Cytoscape Nat. Protoc. 2 2007 2366 2382
4. P.F. Davies Hemodynamic shear stress and the endothelium in cardiovascular pathophysiology Nat. Clin. Pract. Cardiovasc. Med. 6 2009 16 26
5. Y. Fang, C. Shi, E. Manduchi, M. Civelek, and P.F. Davies MicroRNA-10a regulation of proinflammatory phenotype in athero-susceptible endothelium in vivo and in vitro Proc. Natl. Acad. Sci. USA 107 2010 13450 13455
6. R.E. Feaver, N.E. Hastings, A. Pryor, and B.R. Blackman GRP78 upregulation by atheroprone shear stress via p38-, alpha2beta1-dependent mechanism in endothelial cells Arterioscler. Thromb. Vasc. Biol. 28 2008 1534 1541
7. A. Ghazalpour, S. Doss, B. Zhang, S. Wang, C. Plaisier, R. Castellanos, A. Brozell, E.E. Schadt, T.A. Drake, A.J. Lusis, and S. Horvath Integrating genetic and network analysis to characterize genes related to mouse weight PLoS Genet. 2 2006 e130
8. G.R. Grant, J. Liu, and C.J. Stoeckert Jr. A practical false discovery rate approach to identifying patterns of differential expression in microarray data Bioinformatics 21 2005 2684 2690
9. W. Huang da, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 4 2009 44 57
10. P. Langfelder, and S. Horvath WGCNA: An R package for weighted correlation network analysis BMC Bioinform. 9 2008 559
11. P. Langfelder, B. Zhang, and S. Horvath Defining clusters from a hierarchical cluster tree: The Dynamic Tree Cut package for R Bioinformatics 24 2008 719 720
12. J.D. Malhotra, and R.J. Kaufman The endoplasmic reticulum and the unfolded protein response Semin. Cell Dev. Biol. 18 2007 716 731
13. A.G. Passerini, D.C. Polacek, C. Shi, N.M. Francesco, E. Manduchi, G. Grant, W.P. Pritchard, S.J. Powell, G. Chang, C. Stoeckert, and P.F. Davies Coexisting pro-inflammatory and anti-oxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta Proc. Natl. Acad. Sci. USA 101 2004 2482 2487
14. D.C. Polacek, A.G. Passerini, C. Shi, N.M. Francesco, E. Manduchi, G.R. Grant, S. Powell, H. Bischof, H. Winkler, C.J. Stoeckert Jr., and P.F. Davies Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA Physiol. Genomics 13 2003 147 156
15. A. Subramanian, P. Tamayo, V.K. Mootha, S. Mukherjee, B.L. Ebert, M.A. Gillette, A. Paulovich, S.L. Pomeroy, T.R. Golub, E.S. Lander, and J.P. Mesirov Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proc. Natl. Acad. Sci. USA 102 2005 15545 15550
16. C.K. Tuggle, Y. Wang, and O. Couture Advances in swine transcriptomics Int. J. Biol. Sci. 3 2007 132 152
17. R.N. Van Gelder, M.E. von Zastrow, A. Yool, W.C. Dement, J.D. Barchas, and J.H. Eberwine Amplified RNA synthesized from limited quantities of heterogeneous cDNA Proc. Natl. Acad. Sci. USA 87 1990 1663 1667
18. R.R. Wilcox Introduction to Robust Estimation and Hypothesis Testing second edn. 2005 Elsevier/Academic Press Amsterdam, Boston
19. A.M. Yip, and S. Horvath Gene network interconnectedness and the generalized topological overlap measure BMC Bioinform. 8 2007 22
20. L. Zeng, A. Zampetaki, A. Margariti, A.E. Pepe, S. Alam, D. Martin, Q. Xiao, W. Wang, Z.G. Jin, G. Cockerill, K. Mori, and Y.S. Li Sustained activation of XBP1 splicing leads to endothelial apoptosis and atherosclerosis development in response to disturbed flow Proc. Natl. Acad. Sci. USA 106 2009 8326 8331
21. B. Zhang, and S. Horvath A general framework for weighted gene co-expression network analysis Stat. Appl. Genet. Mol. Biol. 4 2005 1 45