Goldsmith ZG, Dhanasekaran N: The microrevolution: applications and impacts of microarray technology on molecular biology and medicine (review). International journal of molecular medicine. 2004, 13 (4): 483-495.
CAS
PubMed
Google Scholar
Fan C, Oh DS, Wessels L, Weigelt B, Nuyten DS, Nobel AB, van't Veer LJ, Perou CM: Concordance among gene-expression-based predictors for breast cancer. The New England journal of medicine. 2006, 355 (6): 560-569. 10.1056/NEJMoa052933.
Article
CAS
PubMed
Google Scholar
Seo D, Ginsburg GS, Goldschmidt-Clermont PJ: Gene expression analysis of cardiovascular diseases: novel insights into biology and clinical applications. Journal of the American College of Cardiology. 2006, 48 (2): 227-235. 10.1016/j.jacc.2006.02.070.
Article
CAS
PubMed
Google Scholar
Napoli C, Lerman LO, Sica V, Lerman A, Tajana G, de Nigris F: Microarray analysis: a novel research tool for cardiovascular scientists and physicians. Heart (British Cardiac Society). 2003, 89 (6): 597-604.
Article
CAS
Google Scholar
Tuomisto TT, Binder BR, Yla-Herttuala S: Genetics, genomics and proteomics in atherosclerosis research. Annals of medicine. 2005, 37 (5): 323-332. 10.1080/07853890510011949.
Article
CAS
PubMed
Google Scholar
Liew CC, Ma J, Tang HC, Zheng R, Dempsey AA: The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool. The Journal of laboratory and clinical medicine. 2006, 147 (3): 126-132. 10.1016/j.lab.2005.10.005.
Article
CAS
PubMed
Google Scholar
Burczynski ME, Twine NC, Dukart G, Marshall B, Hidalgo M, Stadler WM, Logan T, Dutcher J, Hudes G, Trepicchio WL, Strahs A, Immermann F, Slonim DK, Dorner AJ: Transcriptional profiles in peripheral blood mononuclear cells prognostic of clinical outcomes in patients with advanced renal cell carcinoma. Clin Cancer Res. 2005, 11 (3): 1181-1189.
CAS
PubMed
Google Scholar
Alberg AJ, Samet JM: Epidemiology of lung cancer. Chest. 2003, 123 (1 Suppl): 21S-49S. 10.1378/chest.123.1_suppl.21S.
Article
PubMed
Google Scholar
Patino WD, Mian OY, Kang JG, Matoba S, Bartlett LD, Holbrook B, Trout HH, Kozloff L, Hwang PM: Circulating transcriptome reveals markers of atherosclerosis. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102 (9): 3423-3428. 10.1073/pnas.0408032102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bennett L, Palucka AK, Arce E, Cantrell V, Borvak J, Banchereau J, Pascual V: Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. The Journal of experimental medicine. 2003, 197 (6): 711-723. 10.1084/jem.20021553.
Article
CAS
PubMed
PubMed Central
Google Scholar
Njolstad I, Arnesen E, Lund-Larsen PG: Smoking, serum lipids, blood pressure, and sex differences in myocardial infarction. A 12-year follow-up of the Finnmark Study. Circulation. 1996, 93 (3): 450-456.
Article
CAS
PubMed
Google Scholar
Qiao Q, Tervahauta M, Nissinen A, Tuomilehto J: Mortality from all causes and from coronary heart disease related to smoking and changes in smoking during a 35-year follow-up of middle-aged Finnish men. European heart journal. 2000, 21 (19): 1621-1626. 10.1053/euhj.2000.2151.
Article
CAS
PubMed
Google Scholar
Edwards R: The problem of tobacco smoking. BMJ (Clinical research ed). 2004, 328 (7433): 217-219. 10.1136/bmj.328.7433.217.
Article
Google Scholar
Tobacco use among adults – United States, 2005. Mmwr. 2006, 55 (42): 1145-1148.
Buttner P, Mosig S, Funke H: Gene expression profiles of T lymphocytes are sensitive to the influence of heavy smoking: A pilot study. Immunogenetics. 2007, 59 (1): 37-43. 10.1007/s00251-006-0177-3.
Article
PubMed
Google Scholar
van Leeuwen DM, Gottschalk RW, van Herwijnen MH, Moonen EJ, Kleinjans JC, van Delft JH: Differential gene expression in human peripheral blood mononuclear cells induced by cigarette smoke and its constituents. Toxicol Sci. 2005, 86 (1): 200-210. 10.1093/toxsci/kfi168.
Article
CAS
PubMed
Google Scholar
Ryder MI, Hyun W, Loomer P, Haqq C: Alteration of gene expression profiles of peripheral mononuclear blood cells by tobacco smoke: implications for periodontal diseases. Oral microbiology and immunology. 2004, 19 (1): 39-49. 10.1046/j.0902-0055.2003.00110.x.
Article
CAS
PubMed
Google Scholar
Lampe JW, Stepaniants SB, Mao M, Radich JP, Dai H, Linsley PS, Friend SH, Potter JD: Signatures of environmental exposures using peripheral leukocyte gene expression: tobacco smoke. Cancer Epidemiol Biomarkers Prev. 2004, 13 (3): 445-453.
CAS
PubMed
Google Scholar
Harvey BG, Heguy A, Leopold PL, Carolan BJ, Ferris B, Crystal RG: Modification of gene expression of the small airway epithelium in response to cigarette smoking. Journal of molecular medicine (Berlin, Germany). 2007, 85 (1): 39-53.
Article
CAS
Google Scholar
Heguy A, O'Connor TP, Luettich K, Worgall S, Cieciuch A, Harvey BG, Hackett NR, Crystal RG: Gene expression profiling of human alveolar macrophages of phenotypically normal smokers and nonsmokers reveals a previously unrecognized subset of genes modulated by cigarette smoking. Journal of molecular medicine (Berlin, Germany). 2006, 84 (4): 318-328.
Article
CAS
Google Scholar
Lodovici M, Luceri C, De Filippo C, Romualdi C, Bambi F, Dolara P: Smokers and passive smokers gene expression profiles: correlation with the DNA oxidation damage. Free radical biology & medicine. 2007, 43 (3): 415-422. 10.1016/j.freeradbiomed.2007.04.018.
Article
CAS
Google Scholar
Maunders H, Patwardhan S, Phillips J, Clack A, Richter A: Human bronchial epithelial cell transcriptome: gene expression changes following acute exposure to whole cigarette smoke in vitro. American journal of physiology. 2007, 292 (5): L1248-1256.
CAS
PubMed
Google Scholar
Alcorta D, Preston G, Munger W, Sullivan P, Yang JJ, Waga I, Jennette JC, Falk R: Microarray studies of gene expression in circulating leukocytes in kidney diseases. Exp Nephrol. 2002, 10 (2): 139-149. 10.1159/000049909.
Article
CAS
PubMed
Google Scholar
Feezor RJ, Baker HV, Mindrinos M, Hayden D, Tannahill CL, Brownstein BH, Fay A, MacMillan S, Laramie J, Xiao W, Moldawer LL, Cobb JP, Laudanski K, Miller-Graziano CL, Maier RV, Schoenfeld D, Davis RW, Tompkins RG, Inflammation and Host Response to Injury, Large-Scale Collaborative Research Program: Whole blood and leukocyte RNA isolation for gene expression analyses. Physiological genomics. 2004, 19 (3): 247-254. 10.1152/physiolgenomics.00020.2004.
Article
CAS
PubMed
Google Scholar
Feezor RJ, Cheng A, Paddock HN, Baker HV, Moldawer LL: Functional genomics and gene expression profiling in sepsis: beyond class prediction. Clin Infect Dis. 2005, 41 (Suppl 7): S427-435. 10.1086/431993.
Article
CAS
PubMed
Google Scholar
Novoradovskaya N, Whitfield ML, Basehore LS, Novoradovsky A, Pesich R, Usary J, Karaca M, Wong WK, Aprelikova O, Fero M, Perou CM, Botstein D, Braman J: Universal Reference RNA as a standard for microarray experiments. BMC Genomics. 2004, 5 (1): 20-10.1186/1471-2164-5-20.
Article
PubMed
PubMed Central
Google Scholar
Cronin M, Ghosh K, Sistare F, Quackenbush J, Vilker V, O'Connell C: Universal RNA reference materials for gene expression. Clin Chem. 2004, 50 (8): 1464-1471. 10.1373/clinchem.2004.035675.
Article
CAS
PubMed
Google Scholar
UMD: [http://genome.unc.edu]
Smyth GK, Speed T: Normalization of cDNA microarray data. Methods. 2003, 31 (4): 265-273. 10.1016/S1046-2023(03)00155-5.
Article
CAS
PubMed
Google Scholar
Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences of the United States of America. 2001, 98 (9): 5116-5121. 10.1073/pnas.091062498.
Article
CAS
PubMed
PubMed Central
Google Scholar
Storey JD, Tibshirani R: Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods Mol Biol. 2003, 224: 149-157.
CAS
PubMed
Google Scholar
Yu H, Gao L, Tu K, Guo Z: Broadly predicting specific gene functions with expression similarity and taxonomy similarity. Gene. 2005, 352: 75-81. 10.1016/j.gene.2005.03.033.
Article
CAS
PubMed
Google Scholar
Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 1998, 95: 14863-14868. 10.1073/pnas.95.25.14863.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cluster. [http://rana.lbl.gov/EisenSoftware.htm]
Saldanha AJ: Java Treeview – extensible visualization of microarray data. Bioinformatics (Oxford, England). 2004, 20 (17): 3246-3248. 10.1093/bioinformatics/bth349.
Article
CAS
Google Scholar
JavaTreeview. [http://sourceforge.net/projects/jtreeview/]
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102 (43): 15545-15550. 10.1073/pnas.0506580102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Efron B, Tibshirani R: On Testing the Significance of Gene Sets. 2006, Stanford Biostatistics Department
Google Scholar
Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP: GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics (Oxford, England). 2007, 23 (23): 3251-3253. 10.1093/bioinformatics/btm369.
Article
CAS
Google Scholar
The Gene Ontology. [http://www.geneontology.org/]
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chang JT, Nevins JR: GATHER: a systems approach to interpreting genomic signatures. Bioinformatics (Oxford, England). 2006, 22 (23): 2926-2933. 10.1093/bioinformatics/btl483.
Article
CAS
Google Scholar
GATHER- Gene Annotation To Help Explain Relationships.
Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Münch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic acids research. 2003, 31 (1): 374-378. 10.1093/nar/gkg108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic acids research. 2006, D108-110. 10.1093/nar/gkj143. 34 Database
Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhäuser R, Prüss M, Schacherer F, Thiele S, Urbach S: The TRANSFAC system on gene expression regulation. Nucleic acids research. 2001, 29 (1): 281-283. 10.1093/nar/29.1.281.
Article
CAS
PubMed
PubMed Central
Google Scholar
TransFac. [http://www.biobase-international.com/pages/index.php?id=transfac]
Lee KM, Kim JH, Kang D: Design issues in toxicogenomics using DNA microarray experiment. Toxicology and applied pharmacology. 2005, 207 (2S): 200-208. 10.1016/j.taap.2005.01.045.
Article
PubMed
Google Scholar
Cowling DW, Johnson TP, Holbrook BC, Warnecke RB, Tang H: Improving the self reporting of tobacco use: results of a factorial experiment. Tobacco control. 2003, 12 (2): 178-183. 10.1136/tc.12.2.178.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baron-Epel O, Haviv-Messika A, Green MS, Kalutzki DN: Ethnic differences in reported smoking behaviors in face-to-face and telephone interviews. European journal of epidemiology. 2004, 19 (7): 679-686. 10.1023/B:EJEP.0000036792.58923.75.
Article
PubMed
Google Scholar
Payne CE, Southern SJ: Urinary point-of-care test for smoking in the pre-operative assessment of patients undergoing elective plastic surgery. J Plast Reconstr Aesthet Surg. 2006, 59 (11): 1156-1161. 10.1016/j.bjps.2005.12.053.
Article
CAS
PubMed
Google Scholar
Bramer SL, Kallungal BA: Clinical considerations in study designs that use cotinine as a biomarker. Biomarkers. 2003, 8 (3–4): 187-203. 10.1080/13547500310012545.
Article
CAS
PubMed
Google Scholar
Wells AJ, English PB, Posner SF, Wagenknecht LE, Perez-Stable EJ: Misclassification rates for current smokers misclassified as nonsmokers. American journal of public health. 1998, 88 (10): 1503-1509.
Article
CAS
PubMed
PubMed Central
Google Scholar
Recillas-Targa F, De La Rosa-Velazquez IA, Soto-Reyes E, Benitez-Bribiesca L: Epigenetic boundaries of tumour suppressor gene promoters: the CTCF connection and its role in carcinogenesis. Journal of cellular and molecular medicine. 2006, 10 (3): 554-568. 10.1111/j.1582-4934.2006.tb00420.x.
Article
CAS
PubMed
Google Scholar
Torrano V, Chernukhin I, Docquier F, D'Arcy V, Leon J, Klenova E, Delgado MD: CTCF regulates growth and erythroid differentiation of human myeloid leukemia cells. The Journal of biological chemistry. 2005, 280 (30): 28152-28161. 10.1074/jbc.M501481200.
Article
CAS
PubMed
Google Scholar
Rimkus C, Martini M, Friederichs J, Rosenberg R, Doll D, Siewert JR, Holzmann B, Janssen KP: Prognostic significance of downregulated expression of the candidate tumour suppressor gene SASH1 in colon cancer. British journal of cancer. 2006, 95 (10): 1419-1423. 10.1038/sj.bjc.6603452.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barlic J, Zhang Y, Foley JF, Murphy PM: Oxidized lipid-driven chemokine receptor switch, CCR2 to CX3CR1, mediates adhesion of human macrophages to coronary artery smooth muscle cells through a peroxisome proliferator-activated receptor gamma-dependent pathway. Circulation. 2006, 114 (8): 807-819. 10.1161/CIRCULATIONAHA.105.602359.
Article
CAS
PubMed
Google Scholar
Rothbarth K, Spiess E, Juodka B, Yavuzer U, Nehls P, Stammer H, Werner D: Induction of apoptosis by overexpression of the DNA-binding and DNA-PK-activating protein C1D. Journal of cell science. 1999, 112 (Pt 13): 2223-2232.
CAS
PubMed
Google Scholar
Barry WT, Nobel AB, Wright FA: Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics (Oxford, England). 2005, 21 (9): 1943-1949. 10.1093/bioinformatics/bti260.
Article
CAS
Google Scholar
Grumelli S, Corry DB, Song LZ, Song L, Green L, Huh J, Hacken J, Espada R, Bag R, Lewis DE, Kheradmand F: An immune basis for lung parenchymal destruction in chronic obstructive pulmonary disease and emphysema. PLoS medicine. 2004, 1 (1): e8-10.1371/journal.pmed.0010008.
Article
PubMed
PubMed Central
Google Scholar
Chang TK, Chen J, Pillay V, Ho JY, Bandiera SM: Real-time polymerase chain reaction analysis of CYP1B1 gene expression in human liver. Toxicol Sci. 2003, 71 (1): 11-19. 10.1093/toxsci/71.1.11.
Article
CAS
PubMed
Google Scholar
Port JL, Yamaguchi K, Du B, De Lorenzo M, Chang M, Heerdt PM, Kopelovich L, Marcus CB, Altorki NK, Subbaramaiah K, Dannenberg AJ: Tobacco smoke induces CYP1B1 in the aerodigestive tract. Carcinogenesis. 2004, 25 (11): 2275-2281. 10.1093/carcin/bgh243.
Article
CAS
PubMed
Google Scholar
van Leeuwen DM, van Agen E, Gottschalk RW, Vlietinck R, Gielen M, van Herwijnen MH, Maas LM, Kleinjans JC, van Delft JH: Cigarette smoke-induced differential gene expression in blood cells from monozygotic twin pairs. Carcinogenesis. 2007, 28 (3): 691-697. 10.1093/carcin/bgl199.
Article
CAS
PubMed
Google Scholar
Finnstrom N, Ask B, Dahl ML, Gadd M, Rane A: Intra-individual variation and sex differences in gene expression of cytochromes P450 in circulating leukocytes. The pharmacogenomics journal. 2002, 2 (2): 111-116. 10.1038/sj.tpj.6500086.
Article
CAS
PubMed
Google Scholar
Tatone C, Carbone MC, Falone S, Aimola P, Giardinelli A, Caserta D, Marci R, Pandolfi A, Ragnelli AM, Amicarelli F: Age-dependent changes in the expression of superoxide dismutases and catalase are associated with ultrastructural modifications in human granulosa cells. Molecular human reproduction. 2006, 12 (11): 655-660. 10.1093/molehr/gal080.
Article
CAS
PubMed
Google Scholar
Sandler DP, Shore DL, Anderson JR, Davey FR, Arthur D, Mayer RJ, Silver RT, Weiss RB, Moore JO, Schiffer CA, Wurster-Hill DH, McIntyre OR, Bloomfield CD: Cigarette smoking and risk of acute leukemia: associations with morphology and cytogenetic abnormalities in bone marrow. Journal of the National Cancer Institute. 1993, 85 (24): 1994-2003. 10.1093/jnci/85.24.1994.
Article
CAS
PubMed
Google Scholar
Lichtman MA: Cigarette smoking, cytogenetic abnormalities, and acute myelogenous leukemia. Leukemia. 2007, 21 (6): 1137-1140. 10.1038/sj.leu.2404698.
Article
CAS
PubMed
Google Scholar
Newcomb PA, Carbone PP: The health consequences of smoking. Cancer. The Medical clinics of North America. 1992, 76 (2): 305-331.
Article
CAS
PubMed
Google Scholar
Lynge E, Anttila A, Hemminki K: Organic solvents and cancer. Cancer Causes Control. 1997, 8 (3): 406-419. 10.1023/A:1018461406120.
Article
CAS
PubMed
Google Scholar
Gene Set Enrichment Analysis. [http://www.broad.mit.edu/gsea/]
MSigDB Death_Pathway. [http://www.broad.mit.edu/gsea/msigdb/cards/DEATHPATHWAY.html]
MSigDB METASTASIS_ADENOCARC_DN. [http://www.broad.mit.edu/gsea/msigdb/cards/METASTASIS_ADENOCARC_DN.html]
MSigDB DAC_IFN_BLADDER_UP. [http://www.broad.mit.edu/gsea/msigdb/cards/DAC_IFN_BLADDER_UP.html]