Potentials and pitfalls of DNA array analysis of the endothelial stress response

Biochimica et Biophysica Acta - Molecular Cell Research

Volumn 1746, Issue 2, 2005, Pages 73-84

  Viemann, Dorothee ^a   Schulze Osthoff, Klaus ^b   Roth, Johannes ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Endothelial cell; Gene expression; Inflammation; Microarray; Transcription

Indexed keywords

BIOINFORMATICS; CIGARETTE SMOKING; DATA BASE; DNA MICROARRAY; DNA SYNTHESIS; ENDOTHELIUM CELL; GENE EXPRESSION; GENE INDUCTION; GENETIC HETEROGENEITY; GENETIC TRANSCRIPTION; HUMAN; IMMUNE RESPONSE; INFLAMMATION; MEDICAL RESEARCH; MUTATION; NONHUMAN; OUTCOMES RESEARCH; PHENOTYPE; PRIORITY JOURNAL; PROTEIN EXPRESSION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; STRESS;

BIOTECHNOLOGY; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; ENDOTHELIUM, VASCULAR; GENE EXPRESSION PROFILING; HUMANS; INFLAMMATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; STRESS, MECHANICAL;

EID: 28844436037     PISSN: 01674889     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamcr.2005.09.005     Document Type: Review

References (78)

1. F.H. Bach, W.W. Hancock, and C. Ferran Protective genes expressed in endothelial cells: a regulatory response to injury Immunol. Today 18 1997 483 486
2. J. Hawiger Innate immunity and inflammation: a transcriptional paradigm Immunol. Res. 23 2001 99 109
3. A.B. Lentsch, and P.A. Ward Regulation of inflammatory vascular damage J. Pathol. 190 2000 343 348
4. J.M. Cook-Mills, and T.L. Deem Active participation of endothelial cells in inflammation J. Leukoc. Biol. 77 2005 487 495
5. J.S. Pober Immunobiology of human vascular endothelium Immunol. Res. 19 1999 225 232
6. 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
7. B. Zhao, S.A. Stavchansky, R.A. Bowden, and P.D. Bowman Effect of interleukin-1beta and tumor necrosis factor-alpha on gene expression in human endothelial cells Am. J. Physiol., Cell. Physiol. 284 2003 C1577 C1583
8. J. Quackenbush Microarray data normalization and transformation Nat. Genet. 32 2002 496 501 (Suppl.)
9. N. Novoradovskaya, M.L. Whitfield, L.S. Basehore, A. Novoradovsky, R. Pesich, J. Usary, M. Karaca, W.K. Wong, O. Aprelikova, M. Fero, C.M. Perou, D. Botstein, and J. Braman Universal Reference RNA as a standard for microarray experiments BMC Genomics 5 2004 20
10. B. Eickhoff, B. Korn, M. Schick, A. Poustka, and B.J. van der Bosch Normalization of array hybridization experiments in differential gene expression analysis Nucleic Acids Res. 27 1999 e33
11. C. Li, and W. Hung-Wong Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application Genome Biol. 2 2001 (RESEARCH0032)
12. B.M. Bolstad, R.A. Irizarry, M. Astrand, and T.P. Speed A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 19 2003 185 193
13. T.R. Golub, D.K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J.P. Mesirov, H. Coller, M.L. Loh, J.R. Downing, M.A. Caligiuri, C.D. Bloomfield, and E.S. Lander Molecular classification of cancer: class discovery and class prediction by gene expression monitoring Science 286 1999 531 537
14. A. Butte The use and analysis of microarray data Nat. Rev., Drug Discov. 1 2002 951 960
15. M.B. Eisen, P.T. Spellman, P.O. Brown, and D. Botstein Cluster analysis and display of genome-wide expression patterns Proc. Natl. Acad. Sci. U. S. A. 95 1998 14863 14868
16. A.J. Butte, P. Tamayo, D. Slonim, T.R. Golub, and I.S. Kohane Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks Proc. Natl. Acad. Sci. U. S. A. 97 2000 12182 12186
17. V.G. Tusher, R. Tibshirani, and G. Chu Significance analysis of microarrays applied to the ionizing radiation response Proc. Natl. Acad. Sci. U. S. A. 98 2001 5116 5121
18. O. Larsson, C. Wahlestedt, and J.A. Timmons Considerations when using the significance analysis of microarrays (SAM) algorithm BMC Bioinformatics 6 2005 129
19. M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori The KEGG resource for deciphering the genome Nucleic Acids Res. 32 2004 D277 D280
20. I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I.T. Paulsen, M. Peralta-Gil, and P.D. Karp EcoCyc: a comprehensive database resource for Escherichia coli Nucleic Acids Res. 33 2005 D334 D337 (Database issue)
21. J. Papin, and S. Subramaniam Bioinformatics and cellular signaling Curr. Opin. Biotechnol. 15 2004 78 81
22. P.M. Haverty, M.C. Frith, and Z. Weng CARRIE web service: automated transcriptional regulatory network inference and interactive analysis Nucleic Acids Res. 32 2004 W213 W216
23. M. Kankainen, and L. Holm POBO, transcription factor binding site verification with bootstrapping Nucleic Acids Res. 32 2004 W222 W229
24. S. Karanam, and C.S. Moreno CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets Nucleic Acids Res. 32 2004 W475 W484
25. S. Knudsen, C. Workman, T. Sicheritz-Ponten, and C. Friis GenePublisher: Automated analysis of DNA microarray data Nucleic Acids Res. 31 2003 3471 3476
26. B. Zhao, R.A. Bowden, S.A. Stavchansky, and P.D. Bowman Human endothelial cell response to gram-negative lipopolysaccharide assessed with cDNA microarrays Am. J. Physiol., Cell. Physiol. 281 2001 C1587 C1595
27. E.A. Albrecht, A.M. Chinnaiyan, S. Varambally, C. Kumar-Sinha, T.R. Barrette, J.V. Sarma, and P.A. Ward C5a-induced gene expression in human umbilical vein endothelial cells Am. J. Pathol. 164 2004 849 859
28. B. Franzen, K. Duvefelt, C. Jonsson, B. Engelhardt, J. Ottervald, M. Wickman, Y. Yang, and I. Schuppe-Koistinen Gene and protein expression profiling of human cerebral endothelial cells activated with tumor necrosis factor-alpha Brain Res. Mol. Brain Res. 115 2003 130 146
29. T. Murakami, C. Mataki, C. Nagao, M. Umetani, Y. Wada, M. Ishii, S. Tsutsumi, T. Kohro, A. Saiura, H. Aburatani, T. Hamakubo, and T. Kodama The gene expression profile of human umbilical vein endothelial cells stimulated by tumor necrosis factor alpha using DNA microarray analysis J. Atheroscler. Thromb. 7 2000 39 44
30. D. Viemann, M. Goebeler, S. Schmid, K. Klimmek, C. Sorg, S. Ludwig, and J. Roth Transcriptional profiling of IKK2/NF-kappa B- and p38 MAP kinase-dependent gene expression in TNF-alpha-stimulated primary human endothelial cells Blood 103 2004 3365 3373
31. J. Zhou, Y. Jin, Y. Gao, H. Wang, G. Hu, Y. Huang, Q. Chen, M. Feng, and C. Wu Genomic-scale analysis of gene expression profiles in TNF-alpha treated human umbilical vein endothelial cells Inflamm. Res. 51 2002 332 341
32. S.M. McCormick, S.G. Eskin, L.V. McIntire, C.L. Teng, C.M. Lu, C.G. Russell, and K.K. Chittur DNA microarray reveals changes in gene expression of shear stressed human umbilical vein endothelial cells Proc. Natl. Acad. Sci. U. S. A. 98 2001 8955 8960
33. N. Ohura, K. Yamamoto, S. Ichioka, T. Sokabe, H. Nakatsuka, A. Baba, M. Shibata, T. Nakatsuka, K. Harii, Y. Wada, T. Kohro, T. Kodama, and J. Ando Global analysis of shear stress-responsive genes in vascular endothelial cells J. Atheroscler. Thromb. 10 2003 304 313
34. R.J. Dekker, S. van Soest, R.D. Fontijn, S. Salamanca, P.G. de Groot, E. VanBavel, H. Pannekoek, and A.J. Horrevoets Prolonged fluid shear stress induces a distinct set of endothelial cell genes, most specifically lung Kruppel-like factor (KLF2) Blood 100 2002 1689 1698
35. N.G. Abraham, G. Scapagnini, and A. Kappas Human heme oxygenase: cell cycle-dependent expression and DNA microarray identification of multiple gene responses after transduction of endothelial cells J. Cell. Biochem. 90 2003 1098 1111
36. S. Zhang, I.N. Day, and S. Ye Microarray analysis of nicotine-induced changes in gene expression in endothelial cells Physiol. Genomics 5 2001 187 192
37. D. Viemann, A. Strey, A. Janning, K. Jurk, K. Klimmek, T. Vogl, K. Hirono, F. Ichida, D. Foell, B. Kehrel, V. Gerke, C. Sorg, and J. Roth Myeloid-related protein 8 and 14 induce a specific inflammatory response in human microvascular endothelial cells Blood 105 2005 2955 2962
38. U.M. Chandrasekharan, L. Yang, A. Walters, P. Howe, and P.E. DiCorleto Role of CL-100, a dual specificity phosphatase, in thrombin-induced endothelial cell activation J. Biol. Chem. 279 2004 46678 46685
39. A. Matussek, J. Lauber, A. Bergau, W. Hansen, M. Rohde, K.E. Dittmar, M. Gunzer, M. Mengel, P. Gatzlaff, M. Hartmann, J. Buer, and F. Gunzer Molecular and functional analysis of Shiga toxin-induced response patterns in human vascular endothelial cells Blood 102 2003 1323 1332
40. P. Munro, G. Flatau, A. Doye, L. Boyer, O. Oregioni, J.L. Mege, L. Landraud, and E. Lemichez Activation and proteasomal degradation of rho GTPases by cytotoxic necrotizing factor-1 elicit a controlled inflammatory response J. Biol. Chem. 279 2004 35849 35857
41. N. Takeda, K. Maemura, Y. Imai, T. Harada, D. Kawanami, T. Nojiri, I. Manabe, and R. Nagai Endothelial PAS domain protein 1 gene promotes angiogenesis through the transactivation of both vascular endothelial growth factor and its receptor, Flt-1 Circ. Res. 95 2004 146 153
42. A.M. Siwkowski, L.A. Madge, S. Koo, E.L. McMillan, B.P. Monia, J.S. Pober, and B.F. Baker Effects of antisense oligonucleotide-mediated depletion of tumor necrosis factor (TNF) receptor 1-associated death domain protein on TNF-induced gene expression Mol. Pharmacol. 66 2004 572 579
43. N. Torpey, S.E. Maher, A.L. Bothwell, and J.S. Pober Interferon alpha but not interleukin 12 activates STAT4 signaling in human vascular endothelial cells J. Biol. Chem. 279 2004 26789 26796
44. T. Ota, M. Fujii, T. Sugizaki, M. Ishii, K. Miyazawa, H. Aburatani, and K. Miyazono Targets of transcriptional regulation by two distinct type I receptors for transforming growth factor-beta in human umbilical vein endothelial cells J. Cell. Physiol. 193 2002 299 318
45. H. Mayer, M. Bilban, V. Kurtev, F. Gruber, O. Wagner, B.R. Binder, and R. de Martin Deciphering regulatory patterns of inflammatory gene expression from interleukin-1-stimulated human endothelial cells Arterioscler., Thromb., Vasc. Biol. 24 2004 1192 1198
46. The Tumor Analysis Best Practices Working Group Expression profiling-best practices for data generation and interpretation in clinical trials Nat. Rev., Genet. 5 2004 229 237
47. M. Benito, J. Parker, Q. Du, J. Wu, D. Xiang, C.M. Perou, and J.S. Marron Adjustment of systematic microarray data biases Bioinformatics 20 2004 105 114
48. G.A. Churchill Fundamentals of experimental design for cDNA microarrays Nat. Genet. 32 2002 490 495 (Suppl.)
49. P.J. Giles, and D. Kipling Normality of oligonucleotide microarray data and implications for parametric statistical analyses Bioinformatics 19 2003 2254 2262
50. G.W. Hatfield, S.P. Hung, and P. Baldi Differential analysis of DNA microarray gene expression data Mol. Microbiol. 47 2003 871 877
51. J. Seo, M. Bakay, Y.W. Chen, S. Hilmer, B. Shneiderman, and E.P. Hoffman Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection P value weighting in Affymetrix microarrays Bioinformatics 20 2004 2534 2544
52. P.K. Tan, T.J. Downey, E.L. Spitznagel Jr., P. Xu, D. Fu, D.S. Dimitrov, R.A. Lempicki, B.M. Raaka, and M.C. Cam Evaluation of gene expression measurements from commercial microarray platforms Nucleic Acids Res. 31 2003 5676 5684
53. D.A. Lacorre, E.S. Baekkevold, I. Garrido, P. Brandtzaeg, G. Haraldsen, F. Amalric, and J.P. Girard Plasticity of endothelial cells: rapid dedifferentiation of freshly isolated high endothelial venule endothelial cells outside the lymphoid tissue microenvironment Blood 103 2004 4164 4172
54. M.S. Rajeevan, D.G. Ranamukhaarachchi, S.D. Vernon, and E.R. Unger Use of real-time quantitative PCR to validate the results of cDNA array and differential display PCR technologies Methods 25 2001 443 451
55. M.S. Rajeevan, S.D. Vernon, N. Taysavang, and E.R. Unger Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR J. Mol. Diagn. 3 2001 26 31
56. R.F. Chuaqui, R.F. Bonner, C.J. Best, J.W. Gillespie, M.J. Flaig, S.M. Hewitt, J.L. Phillips, D.B. Krizman, M.A. Tangrea, M. Ahram, W.M. Linehan, V. Knezevic, and M.R. Emmert-Buck Post-analysis follow-up and validation of microarray experiments Nat. Genet. 32 2002 509 514 (Suppl)
57. D. Gomez, and N.C. Reich Stimulation of primary human endothelial cell proliferation by IFN J. Immunol. 170 2003 5373 5381
58. I.M. Cristea, S.J. Gaskell, and A.D. Whetton Proteomics techniques and their application to hematology Blood 103 2004 3624 3634
59. J.E. Celis, M. Ostergaard, N.A. Jensen, I. Gromova, H.H. Rasmussen, and P. Gromov Human and mouse proteomic databases: novel resources in the protein universe FEBS Lett. 430 1998 64 72
60. A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball, H.C. Causton, T. Gaasterland, P. Glenisson, F.C. Holstege, I.F. Kim, V. Markowitz, J.C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo, and M. Vingron Minimum information about a microarray experiment (MIAME)-toward standards for microarray data Nat. Genet. 29 2001 365 371
61. C.J. Stoeckert Jr., H.C. Causton, and C.A. Ball Microarray databases: standards and ontologies Nat. Genet. 32 2002 469 473 (Suppl.)
62. L. Huminiecki, A.T. Lloyd, and K.H. Wolfe Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases BMC Genomics 4 2003 31
63. C.J. Miller, and T.K. Attwood Bioinformatics goes back to the future Nat. Rev., Mol. Cell Biol. 4 2003 157 162
64. V.R. Iyer, C.E. Horak, C.S. Scafe, D. Botstein, M. Snyder, and P.O. Brown Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF Nature 409 2001 533 538
65. B. Ren, F. Robert, J.J. Wyrick, O. Aparicio, E.G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T.L. Volkert, C.J. Wilson, S.P. Bell, and R.A. Young Genome-wide location and function of DNA binding proteins Science 290 2000 2306 2309
66. F. Al Shahrour, R. Diaz-Uriarte, and J. Dopazo FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes Bioinformatics 20 2004 578 580
67. F. Al Shahrour, R. Diaz-Uriarte, and J. Dopazo Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information Bioinformatics 21 2005 2988 2993
68. K.H. Cheung, R. de Knikker, Y. Guo, G. Zhong, J. Hager, K.Y. Yip, A.K. Kwan, P. Li, and D.W. Cheung Biosphere: the interoperation of web services in microarray cluster analysis Appl. Bioinformatics 3 2004 253 256
69. H.J. Chung, M. Kim, C.H. Park, J. Kim, and J.H. Kim ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics Nucleic Acids Res. 32 2004 W460 W464
70. M. Masseroli, D. Martucci, and F. Pinciroli GFINDer: Genome Function Integrated Discoverer through dynamic annotation, statistical analysis, and mining Nucleic Acids Res. 32 2004 W293 W300
71. C. Pasquier, F. Girardot, d.F. Jevardat, and R. Christen THEA: ontology-driven analysis of microarray data Bioinformatics 20 2004 2636 2643
72. S. Volinia, R. Evangelisti, F. Francioso, D. Arcelli, M. Carella, and P. Gasparini GOAL: automated Gene Ontology analysis of expression profiles Nucleic Acids Res. 32 2004 W492 W499
73. B. Coessens, G. Thijs, S. Aerts, K. Marchal, F. De Smet, K. Engelen, P. Glenisson, Y. Moreau, J. Mathys, and B. De Moor INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis Nucleic Acids Res. 31 2003 3468 3470
74. S.W. Doniger, N. Salomonis, K.D. Dahlquist, K. Vranizan, S.C. Lawlor, and B.R. Conklin MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data Genome Biol. 4 2003 R7
75. J. Herrero, F. Al Shahrour, R. Diaz-Uriarte, A. Mateos, J.M. Vaquerizas, J. Santoyo, and J. Dopazo GEPAS: A web-based resource for microarray gene expression data analysis Nucleic Acids Res. 31 2003 3461 3467
76. J. Herrero, J.M. Vaquerizas, F. Al Shahrour, L. Conde, A. Mateos, J.S. Diaz-Uriarte, and J. Dopazo New challenges in gene expression data analysis and the extended GEPAS Nucleic Acids Res. 32 2004 W485 W491
77. N.M. Luscombe, T.E. Royce, P. Bertone, N. Echols, C.E. Horak, J.T. Chang, M. Snyder, and M. Gerstein expressyourself: a modular platform for processing and visualizing microarray data Nucleic Acids Res. 31 2003 3477 3482
78. S. Zhong, C. Li, and W.H. Wong ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis Nucleic Acids Res. 31 2003 3483 3486