Orthologous gene-expression profiling in multi-species models: search for candidate genes

Genome Biology

Volumn 5, Issue 5, 2004, Pages

  Grigoryev, Dmitry N ^a   Ma, Shwu Fan ^a   Irizarry, Rafael A ^b   Ye, Shui Qing ^b   Quackenbush, John ^c   Garcia, Joe Gn ^b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

Author keywords

Acute Lung Injury; Additional Data File; Gene Ontology; Mechanical Stretch; U133A Array

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CELL LINE; CHEMISTRY; COMPARATIVE STUDY; CYTOLOGY; DISEASE MODEL; DNA MICROARRAY; DOG; ENDOTHELIUM; GENE; GENE EXPRESSION PROFILING; GENETICS; HUMAN; LUNG; LUNG DISEASE; METABOLISM; METHODOLOGY; MOUSE; RAT; SPECIES DIFFERENCE; STATISTICS;

ANIMALS; CELL LINE; DISEASE MODELS, ANIMAL; DOGS; ENDOTHELIUM; GENE EXPRESSION PROFILING; GENES; HUMANS; LUNG; LUNG DISEASES; MICE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RATS; SPECIES SPECIFICITY;

EID: 4644262045     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2004-5-5-r34     Document Type: Article

References (54)

1. The Acute Respiratory Distress Syndrome Network: Ventilation with lower tidal volumes as compared with traditional tidal volumes for acute lung injury and the acute respiratory distress syndrome. N Engl J Med. 2000, 342: 1301-1308. 10.1056/NEJM200005043421801. DOI: 10.1056/NEJM200005043421801
2. Parker JC: Inhibitors of myosin light chain kinase and phosphodiesterase reduce ventilator-induced lung injury. J Appl Physiol. 2000, 89: 2241-2248.
3. Parker JC, Ivey CL, Tucker A: Phosphotyrosine phosphatase and tyrosine kinase inhibition modulate airway pressure-induced lung injury. J Appl Physiol. 1998, 85: 1753-1761.
4. Webb HH, Tierney DF: Experimental pulmonary edema due to intermittent positive pressure ventilation with high inflation pressures. Protection by positive end-expiratory pressure. Am Rev Respir Dis. 1974, 110: 556-565.
5. Parker JC, Ivey CL, Tucker JA: Gadolinium prevents high airway pressure-induced permeability increases in isolated rat lungs. J Appl Physiol. 1998, 84: 1113-1118. 10.1063/1.368111. DOI: 10.1063/1.368111
6. Khimenko PL, Moore TM, Wilson PS, Taylor AE: Role of calmodulin and myosin light-chain kinase in lung ischemia-reperfusion injury. Am J Physiol. 1996, 271: L121-L125.
7. Villar J, Flores C, Mendez-Alvarez S: Genetic susceptibility to acute lung injury. Crit Care Med. 2003, 31 (4 Suppl): S272-S275. DOI: 10.1097/01.CCM.0000057903.11528.6D
8. Russell JA: Genetics of coagulation factors in acute lung injury. Crit Care Med. 2003, 31 (4 Suppl): S243-S247. DOI: 10.1097/01.CCM.0000057870.61079.3E
9. Garcia J, Nonas S, Kawkitinarong K, Barnes K: SNPs, chips and functional genomics in acute lung injury. Am J Respir Cell Mol Biol.
10. Birukov KG, Jacobson JR, Flores AA, Ye SQ, Birukova AA, Verin AD, Garcia JG: Magnitude-dependent regulation of pulmonary endothelial cell barrier function by cyclic stretch. Am J Physiol Lung Cell Mol Physiol. 2003, 285: L785-L797. DOI: 10.1152/ajplung.00336.2002
11. Ramaswamy S, Ross KN, Lander ES, Golub TR: A molecular signature of metastasis in primary solid tumors. Nat Genet. 2003, 33: 49-54. 10.1038/ng1060. DOI: 10.1038/ng1060
12. Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM: Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res. 2002, 62: 4427-4433.
13. Ghosh D, Barette TR, Rhodes D, Chinnaiyan AM: Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics. 2003, 3: 180-188. 10.1007/s10142-003-0087-5. DOI: 10.1007/s10142-003-0087-5
14. Eukaryotic gene orthologs. [http://www.tigr.org/tdb/tgi/ego]
15. Dubchak I, Brudno M, Loots GG, Pachter L, Mayor C, Rubin EM, Frazer KA: Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 2000, 10: 1304-1306. 10.1101/gr.142200. DOI: 10.1101/gr.142200
16. Frazer KA, Sheehan JB, Stokowski RP, Chen X, Hosseini R, Cheng JF, Fodor SP, Cox DR, Patil N: Evolutionarily conserved sequences on human chromosome 21. Genome Res. 2001, 11: 1651-1659. 10.1101/gr.198201. DOI: 10.1101/gr.198201
17. Tsai J, Sultana R, Lee Y, Pertea G, Karamycheva S, Antonescu V, Cho J, Parvizi B, Cheung F, Quackenbush J: RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biol. 2001, 2: software0002.1-0002.4. 10.1186/gb-2001-2-11-software0002. DOI: 10.1186/gb-2001-2-11-software0002
18. Svensson BA, Kreeft AJ, van Ommen GJ, den Dunnen JT, Boer JM: GeneHopper: a web-based search engine to link gene-expression platforms through GenBank accession numbers. Genome Biol. 2003, 4: R35-10.1186/gb-2003-4-5-r35. DOI: 10.1186/gb-2003-4-5-r35
19. GeneHopper. [http://lgtc.nl/GeneHopper]
20. RESOURCERER.[http://pga.tigr.org/tigr-scripts/magic/r1.pl]
21. Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, et al: Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res. 2002, 12: 493-502. 10.1101/gr.212002. DOI: 10.1101/gr.212002
22. Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, Conklin BR: MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 2003, 4: R7-10.1186/gb-2003-4-1-r7. DOI: 10.1186/gb-2003-4-1-r7
23. GenMAPP homepage.[http://www.genmapp.org]
24. HOPGENE resources. [http://www.hopkins-genomics.org/resources/resourcesSoftware.html]
25. Lagreid A, Hvidsten TR, Midelfart H, Komorowski J, Sandvik AK: Predicting gene ontology biological process from temporal gene expression patterns. Genome Res. 2003, 13: 965-979. 10.1101/gr.1144503. DOI: 10.1101/gr.1144503
26. Gene Ontology Consortium. [http://www.geneontology.org]
27. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR: GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet. 2002, 31: 19-20. 10.1038/ng0502-19. DOI: 10.1038/ng0502-19
28. Kurdowska AK, Geiser TK, Alden SM, Dziadek BR, Noble JM, Nuckton TJ, Matthay MA: Activity of pulmonary edema fluid interleukin-8 bound to alpha(2)-macroglobulin in patients with acute lung injury. Am J Physiol Lung Cell Mol Physiol. 2002, 282: L1092-L1098. DOI: 10.1152/ajplung.00378.2001
29. Elsayed NM, Ellingson AS, Tierney DF, Mustafa MG: Effects of ozone inhalation on polyamine metabolism and tritiated thymidine incorporation into DNA of rat lungs. Toxicol Appl Pharmacol. 1990, 102: 1-8. DOI: 10.1016/0041-008X(90)90078-9
30. Park WY, Goodman RB, Steinberg KP, Ruzinski JT, Radella F, Park DR, Pugin J, Skerrett SJ, Hudson LD, Martin TR: Cytokine balance in the lungs of patients with acute respiratory distress syndrome. Am J Respir Crit Care Med. 2001, 164: 1896-1903. DOI: 10.1164/ajrccm.164.10.2104013
31. Kolb M, Margetts PJ, Anthony DC, Pitossi F, Gauldie J: Transient expression of IL-1beta induces acute lung injury and chronic repair leading to pulmonary fibrosis. J Clin Invest. 2001, 107: 1529-1536. DOI: 10.1172/JCI12568
32. Chess PR, Johnston CJ, Wright TW, Jordan HD: Murine model of mechanical ventilation-induced lung injury. Am J Respir Crit Care Med. 2003, 167: A625-
33. Takala A, Jousela I, Takkunen O, Kautiainen H, Jansson SE, Orpana A, Karonen SL, Repo H: A prospective study of inflammation markers in patients at risk of indirect acute lung injury. Shock. 2002, 17: 252-257. 10.1097/00024382-200204000-00002. DOI: 10.1097/00024382-200204000-00002
34. Gust R, Kozlowski JK, Stephenson AH, Schuster DP: Role of cyclooxygenase-2 in oleic acid-induced acute lung injury. Am J Respir Crit Care Med. 1999, 160: 1165-1170. DOI: 10.1164/ajrccm.160.4.9811073
35. Enkhbaatar P, Murakami K, Shimoda K, Chandra A, Traber L, Hawkins H, Herndon D, Traber D: Ketorolac, a nonsteroidal anti-inflammatory agent prevents burn/smoke-induced acute lung injury in sheep by inhibiting nitric oxide. Am J Respir Crit Care Med. 2003, 167: A665-10.1164/rccm.200209-1031PP. DOI: 10.1164/ajrccm.167.4.955
36. Cheng IW, Ware LB, Greene KE, Nuckton TJ, Eisner MD, Matthay MA: Prognostic value of surfactant proteins A and D in patients with acute lung injury. Crit Care Med. 2003, 31: 20-27. 10.1097/00003246-200301000-00003. DOI: 10.1097/00003246-200301000-00003
37. He Y, Crouch E: Surfactant protein D gene regulation. Interactions among the conserved CCAAT/enhancer-binding protein elements. J Biol Chem. 2002, 277: 19530-19537. 10.1074/jbc.M201126200. DOI: 10.1074/jbc.M201126200
38. Rosenberg E, Li F, Reisher SR, Wang M, Gonzales LW, Ewing JR, Malek S, Ballard PL, Notarfrancesco K, Shuman H, Feinstein SI: Members of the C/EBP transcription factor family stimulate expression of the human and rat surfactant protein A (SP-A) genes. Biochim Biophys Acta. 2002, 1575: 82-90. 10.1016/S0167-4781(02)00287-7. DOI: 10.1016/S0167-4781(02)00287-7
39. Sugahara K, Sadohara T, Sugita M, Iyama K, Takiguchi M: Differential expression of CCAAT enhancer binding protein family in rat alveolar epithelial cell proliferation and in acute lung injury. Cell Tissue Res. 1999, 297: 261-270. 10.1007/s004410051354. DOI: 10.1007/s004410051354
40. Corne J, Chupp G, Lee CG, Homer RJ, Zhu Z, Chen Q, Ma B, Du Y, Roux F, McArdle J, et al: IL-13 stimulates vascular endothelial cell growth factor and protects against hyperoxic acute lung injury. J Clin Invest. 2000, 106: 783-791. DOI: 10.1172/JCI9674
41. Rose CE, Sung SS, Fu SM: Significant involvement of CCL2 (MCP-1) in inflammatory disorders of the lung. Microcirculation. 2003, 10: 273-288. 10.1038/sj.mn.7800193. DOI: 10.1080/mic.10.3-4.273.288
42. Groeneveld AB, Kindt I, Raijmakers PG, Hack CE, Thijs LG: Systemic coagulation and fibrinolysis in patients with or at risk for the adult respiratory distress syndrome. Thromb Haemost. 1997, 78: 1444-1449.
43. Prabhakaran P, Ware LB, White KE, Cross MT, Matthay MA, Olman MA: Elevated levels of plasminogen activator inhibitor-1 in pulmonary edema fluid are associated with mortality in acute lung injury. Am J Physiol Lung Cell Mol Physiol. 2003, 285: L20-L28. DOI: 10.1152/ajplung.00312.2002
44. Ruf W, Riewald M: Tissue factor-dependent coagulation protease signaling in acute lung injury. Crit Care Med. 2003, 31 (4 Suppl): S231-S237. DOI: 10.1097/01.CCM.0000057848.27456.04
45. Schultz M, Millo J, Levi M, Garrard C, van der Poll T: Local activation of coagulation and inhibition of fibrinolysis in the lung during ventilator-associated pneumonia. Am J Respir Crit Care Med. 2003, 167: A861-
46. Schmidt B, Davis P, La Pointe H, Monkman S, Coates G, deSa D: Thrombin inhibitors reduce intrapulmonary accumulation of fibrinogen and procoagulant activity of bronchoalveolar lavage fluid during acute lung injury induced by pulmonary overdistention in newborn piglets. Pediatr Res. 1996, 39: 798-804. DOI: 10.1203/00006450-199605000-00009
47. Perez RL, Ritzenthaler JD, Roman J: Transcriptional regulation of the interleukin-1beta promoter via fibrinogen engagement of the CD18 integrin receptor. Am J Respir Cell Mol Biol. 1999, 20: 1059-1066. DOI: 10.1165/ajrcmb.20.5.3281
48. Hasegawa T, Sorensen L, Dohi M, Rao NV, Hoidal JR, Marshall BC: Induction of urokinase-type plasminogen activator receptor by IL-1 beta. Am J Respir Cell Mol Biol. 1997, 16: 683-692. DOI: 10.1165/ajrcmb.16.6.9191470
49. Johnson K, Aarden L, Choi Y, De Groot E, Creasey A: The proinflammatory cytokine response to coagulation and endotoxin in whole blood. Blood. 1996, 87: 5051-5060.
50. Johnson K, Choi Y, DeGroot E, Samuels I, Creasey A, Aarden L: Potential mechanisms for a proinflammatory vascular cytokine response to coagulation activation. J Immunol. 1998, 160: 5130-5135.
51. Irizarry R, Gautier L, Cope L: An R package for analyses of Affymetrix oligonucleotide arrays. In The Analysis of Gene Expression Data: Methods and Software. Edited by: Parmigiani G, Garrett ES, Irizarry RA, Zeger SL. 2003, New York: Springer
52. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003, 31: e15-10.1093/nar/gng015. DOI: 10.1093/nar/gng015
53. Chudin E, Walker R, Kosaka A, Wu SX, Rabert D, Chang TK, Kreder DE: Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays. Genome Biol. 2002, 3: research0005.1-0005.10. 10.1186/gb-2001-3-1-research0005.
54. HOPGENE homepage. [http://www.hopkins-genomics.org]