Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Gormley, Michael ^a   Tozeren, Aydin ^a  

^a DREXEL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PHENOTYPES; EXPRESSION PATTERNS; GENE EXPRESSION MICROARRAY; IDENTIFICATION AND ANNOTATION; LARGE-SCALE DATASETS; MODEL-BASED CLASSIFICATIONS; MODEL-BASED CLUSTERING; SUPERVISED CLASSIFICATION;

BIOLOGICAL MEMBRANES; CLASSIFICATION (OF INFORMATION); CLUSTERING ALGORITHMS; ENZYME ACTIVITY; IMMUNE SYSTEM; MUSCLE;

GENE EXPRESSION;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; COMMUNICABLE DISEASE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC MARKER; GENETICS; HUMAN; METHODOLOGY; MOUSE; PHENOTYPE; REGULATOR GENE;

ALGORITHMS; ANIMALS; COMMUNICABLE DISEASES; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENES, SWITCH; GENETIC MARKERS; HUMANS; MICE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE;

EID: 58149479745     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-486     Document Type: Article

References (69)

1. Arora A Simpson DA Individual mRNA expression profiles reveal the effects of specific microRNAs Genome biology 2008, 9(5):R82. 2441468 18485210 10.1186/gb-2008-9-5-r82
2. Hobert O Gene regulation by transcription factors and microRNAs Science (New York, NY) 2008, 319:5871-1785. 1786
3. Jaenisch R Bird A Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals Nature genetics 2003, 33(Suppl):245-254. 10.1038/ng1089 12610534
4. Hsiao LL Dangond F Yoshida T Hong R Jensen RV Misra J Dillon W Lee KF Clark KE Haverty P A et al. compendium of gene expression in normal human tissues Physiological genomics 2001, 7(2):97-104. 11773596
5. Warrington JA Nair A Mahadevappa M Tsyganskaya M Comparison of human adult and fetal expression and identification of 535 housekeeping/ maintenance genes Physiological genomics 2000, 2(3):143-147. 11015593
6. Ertel A Tozeren A Human switch-like genes and their regulation via transcription initiation and histone methylation BMC Genomics 2008 (in review). 2257939 18177501
7. Alizadeh AA Eisen MB Davis RE Ma C Lossos IS Rosenwald A Boldrick JC Sabet H Tran T Yu X et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling Nature 2000, 403:6769-503. 511 10.1038/35000501 10676951
8. Alon U Barkai N Notterman DA Gish K Ybarra S Mack D Levine AJ Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays Proceedings of the National Academy of Sciences of the United States of America 1999, 96(12):6745-6750. 21986 10359783 10.1073/pnas.96.12.6745
9. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proceedings of the National Academy of Sciences of the United States of America 1998, 95(25):14863-14868. 24541 9843981 10.1073/pnas.95.25.14863
10. Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich A Pomeroy SL Golub TR Lander ES et al. 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. 1239896 16199517 10.1073/pnas.0506580102
11. 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. 33173 11309499 10.1073/pnas.091062498
12. van't Veer LJ Dai H Vijver van de MJ He YD Hart AA Mao M Peterse HL Kooy van der K Marton MJ Witteveen AT et al. Gene expression profiling predicts clinical outcome of breast cancer Nature 2002, 415(6871):530-536. 10.1038/415530a 11823860
13. Wang Y Klijn JG Zhang Y Sieuwerts AM Look MP Yang F Talantov D Timmermans M Meijer-van Gelder ME Yu J et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer Lancet 2005, 365(9460):671-679. 15721472
14. West M Blanchette C Dressman H Huang E Ishida S Spang R Zuzan H Olson JA Jr Marks JR Nevins JR Predicting the clinical status of human breast cancer by using gene expression profiles Proceedings of the National Academy of Sciences of the United States of America 2001, 98(20):11462-11467. 58752 11562467 10.1073/pnas.201162998
15. Tavazoie S Hughes JD Campbell MJ Cho RJ Church GM Systematic determination of genetic network architecture Nature genetics 1999, 22(3):281-285. 10.1038/10343 10391217
16. Toronen P Kolehmainen M Wong G Castren E Analysis of gene expression data using self-organizing maps FEBS letters 1999, 451(2):142-146. 10.1016/S0014-5793(99)00524-4 10371154
17. Ghosh D Chinnaiyan AM Mixture modelling of gene expression data from microarray experiments Bioinformatics (Oxford, England) 2002, 18(2):275-286. 10.1093/bioinformatics/18.2.275 11847075
18. McLachlan GJ Bean RW Peel D A mixture model-based approach to the clustering of microarray expression data Bioinformatics (Oxford, England) 2002, 18(3):413-422. 10.1093/bioinformatics/18.3.413 11934740
19. Yeung KY Fraley C Murua A Raftery AE Ruzzo WL Model-based clustering and data transformations for gene expression data Bioinformatics (Oxford, England) 2001, 17(10):977-987. 10.1093/bioinformatics/17.10.977 11673243
20. Joshi A Peer Van de Y Michoel T Analysis of a Gibbs sampler method for model-based clustering of gene expression data Bioinformatics (Oxford, England) 2008, 24(2):176-183. 10.1093/bioinformatics/btm562 18033794
21. Medvedovic M Yeung KY Bumgarner RE Bayesian mixture model based clustering of replicated microarray data Bioinformatics (Oxford, England) 2004, 20(8):1222-1232. 10.1093/bioinformatics/bth068 14871871
22. Qin ZS Clustering microarray gene expression data using weighted Chinese restaurant process Bioinformatics (Oxford, England) 2006, 22(16):1988-1997. 10.1093/bioinformatics/btl284 16766561
23. Hoff PD Model-based subspace clustering Bayesian Analysis 2006, 1(2):321-344
24. Hynes RO Integrins: Bidirectional, allosteric signaling machines Cell 2002, 110(6):673-687. 10.1016/S0092-8674(02)00971-6 12297042
25. Nelson CM Bissell MJ Of extracellular matrix, scaffolds, and signaling: tissue architecture regulates development, homeostasis, and cancer Annual review of cell and developmental biology 2006, 22:287-309. 10.1146/annurev.cellbio.22.010305.104315
26. Bon G Folgiero V Di Carlo S Sacchi A Falcioni R Involvement of alpha6beta4 integrin in the mechanisms that regulate breast cancer progression Breast Cancer Res 2007, 9(1):203. 1851390 17319974 10.1186/ bcr1651
27. Buttery RC Rintoul RC Sethi T Small cell lung cancer: The importance of the extracellular matrix The international journal of biochemistry & cell biology 2004, 36(7):1154-1160. 10.1016/S1357-2725(03)00261-9 15109562
28. van Horssen J Dijkstra CD de Vries HE The extracellular matrix in multiple sclerosis pathology Journal of neurochemistry 2007, 103(4):1293-1301. 10.1111/j.1471-4159.2007.04897.x 17854386
29. Yu WM Yu H Chen ZL Laminins in peripheral nerve development and muscular dystrophy Molecular neurobiology 2007, 35(3):288-297. 10.1007/ s12035-007-0026-x 17917117
30. Yamada S Nelson WJ Synapses: Sites of cell recognition, adhesion, and functional specification Annual review of biochemistry 2007, 76:267-294. 10.1146/annurev.biochem.75.103004.142811 17506641
31. Scherer SS Arroyo EJ Recent progress on the molecular organization of myelinated axons J Peripher Nerv Syst 2002, 7(1):1-12. 10.1046/ j.1529-8027.2002.02001.x 11939347
32. Janeway CA Jr Medzhitov R Innate immune recognition Annual review of immunology 2002, 20:197-216. 10.1146/annurev.immunol.20.083001.084359 11861602
33. Pasare C Medzhitov R Toll-like receptors: Linking innate and adaptive immunity Microbes and infection/Institut Pasteur 2004, 6(15):1382-1387. 15596124
34. Bureau C Bernad J Chaouche N Orfila C Beraud M Gonindard C Alric L Vinel JP Pipy B Nonstructural 3 protein of hepatitis C virus triggers an oxidative burst in human monocytes via activation of NADPH oxidase The Journal of biological chemistry 2001, 276(25):23077-23083. 10.1074/ jbc.M100698200 11304537
35. Guida M D'Elia G Benvestito S Casamassima A Micelli G Quaranta M Moschetta R De Lena M Lorusso V Hepatitis C virus infection in patients with B-cell lymphoproliferative disorders Leukemia 2002, 16(10):2162-2163. 10.1038/sj.leu.2402626 12357374
36. Landau DA Saadoun D Calabrese LH Cacoub P The pathophysiology of HCV induced B-cell clonal disorders Autoimmunity reviews 2007, 6(8):581-587. 10.1016/j.autrev.2007.03.010 17854753
37. Lindenschmidt EG Granato CH Katzner K Laufs R Evidence for limited humoral immunoglobulin M antibody response to hepatitis B core antigen during acute and chronic hepatitis B virus infections Journal of clinical microbiology 1985, 21(6):1000-1003. 271839 3891772
38. Sarantis H Gray-Owen SD The specific innate immune receptor CEACAM3 triggers neutrophil bactericidal activities via a Syk kinase-dependent pathway Cellular microbiology 2007, 9(9):2167-2180. 10.1111/ j.1462-5822.2007.00947.x 17506820
39. Anand AR Ganju RK HIV-1 gp120-mediated apoptosis of T cells is regulated by the membrane tyrosine phosphatase CD45 The Journal of biological chemistry 2006, 281(18):12289-12299. 10.1074/jbc.M511786200 16524887
40. Barat C Tremblay MJ Engagement of CD43 enhances human immunodeficiency virus type 1 transcriptional activity and virus production that is induced upon TCR/CD3 stimulation The Journal of biological chemistry 2002, 277(32):28714-28724. 10.1074/jbc.M111935200 12045189
41. Perfettini JL Roumier T Castedo M Larochette N Boya P Raynal B Lazar V Ciccosanti F Nardacci R Penninger J et al. NF-kappaB and p53 are the dominant apoptosis-inducing transcription factors elicited by the HIV-1 envelope The Journal of experimental medicine 2004, 199(5):629-640. 2213296 14993250 10.1084/jem.20031216
42. Shyamsundar R Kim YH Higgins JP Montgomery K Jorden M Sethuraman A Rijn van de M Botstein D Brown PO Pollack JR A DNA microarray survey of gene expression in normal human tissues Genome biology 2005, 6(3):R22. 1088941 15774023 10.1186/gb-2005-6-3-r22
43. Whitney AR Diehn M Popper SJ Alizadeh AA Boldrick JC Relman DA Brown PO Individuality and variation in gene expression patterns in human blood Proceedings of the National Academy of Sciences of the United States of America 2003, 100(4):1896-1901. 149930 12578971 10.1073/pnas.252784499
44. Yanai I Benjamin H Shmoish M Chalifa-Caspi V Shklar M Ophir R Bar-Even A Horn-Saban S Safran M Domany E et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification Bioinformatics (Oxford, England) 2005, 21(5):650-659. 10.1093/bioinformatics/bti042 15388519
45. Golub TR Slonim DK Tamayo P Huard C Gaasenbeek M Mesirov JP Coller H Loh ML Downing JR Caligiuri MA et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring Science 1999, 286(5439):531-537. 10.1126/science.286.5439.531 10521349
46. Tibshirani R Walther G Hastie T Estimating the number of clusters in a data set via the gap statistic Journal of the Royal Statistical Society Series B-Statistical Methodology 2001, 63:411-423. 10.1111/ 1467-9868.00293
47. Ertel A Tozeren A Switch-like genes populate cell communication pathways and are enriched for extracellular proteins BMC Genomics 2008, 9:3. 2257939 18177501 10.1186/1471-2164-9-3
48. Yeung KY Medvedovic M Bumgarner RE Clustering gene-expression data with repeated measurements Genome Biology 2003, 4:R34. 156590 12734014 10.1186/gb-2003-4-5-r34
49. Thalamuthu A Mukhopadhyay I Zheng X Tseng GC Evaluation and comparision of gene clustering methods in microarray analysis Bioinformatics 2006, 22:2405-2412. 10.1093/bioinformatics/btl406 16882653
50. The Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 2007, 447(7145):661-678. 10.1038/nature05911 17554300
51. Stranger BE Forrest MS Clark AG Minichiello MJ Deutsch S Lyle R Hunt S Kahl B Antonarakis SE Tavare S et al. Genome-wide associations of gene expression variation in humans PLoS genetics 2005, 1(6):e78. 1315281 16362079 10.1371/journal.pgen.0010078
52. Stranger BE Forrest MS Dunning M Ingle CE Beazley C Thorne N Redon R Bird CP de Grassi A Lee C et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes Science 2007, 315(5813):848-853. 10.1126/science.1136678 17289997
53. Edgar R Domrachev M Lash AE Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic acids research 2002, 30(1):207-210. 99122 11752295 10.1093/nar/30.1.207
54. Parkinson H Kapushesky M Shojatalab M Abeygunawardena N Coulson R Farne A Holloway E Kolesnykov N Lilja P Lukk M et al. ArrayExpress - a public database of microarray experiments and gene expression profiles Nucleic acids research 2007. 35 Database D747-750. 1716725 17132828 10.1093/nar/ gkl995
55. Katz S Irizarry RA Lin X Tripputi M Porter MW A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database BMC bioinformatics 2006, 7:464. 1624855 17059591 10.1186/1471-2105-7-464
56. Irizarry RA Hobbs B Collin F Beazer-Barclay YD Antonellis KJ Scherf U Speed TP Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics (Oxford, England) 2003, 4(2):249-264. 12925520
57. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nature genetics 2000, 25(1):25-29. 10.1038/75556 10802651
58. Kanehisa M Goto S KEGG: Kyoto encyclopedia of genes and genomes Nucleic acids research 2000, 28(1):27-30. 102409 10592173 10.1093/nar/28.1.27
59. Fan J May SJ Zhou Y Barrett-Connor E Bimodality of 2-h plasma glucose distributions in whites: The Rancho Bernardo study Diabetes care 2005, 28(6):1451-1456. 10.2337/diacare.28.6.1451 15920067
60. Lim TO Bakri R Morad Z Hamid MA Bimodality in blood glucose distribution: Is it universal? Diabetes care 2002, 25(12):2212-2217. 10.2337/diacare.25.12.2212 12453963
61. Maclean CJ Morton NE Elston RC Yee S Skewness in commingled distributions Biometrics 1976, 32(3):695-699. 10.2307/2529760 963179
62. Dempster AP Laird NM Rubin DB Maximum likelihood from incomplete data via the EM alogrithm Journal of the Royal Statistical Society 1977, 39:1-38
63. Zhang B Kirov S Snoddy J WebGestalt: An integrated system for exploring gene sets in various biological contexts Nucleic acids research 2005, 33 Web Server W741-748. 1160236 15980575 10.1093/nar/gki475
64. Hartigan JA Wong MA A K-means clustering algorithm Applied Statistics 1979, 28:100-108. 10.2307/2346830
65. Gibbons FD Roth FP Judging the quality of gene expression-based clustering methods using gene annotation Genome Research 2002, 12:1574-1581. 187526 12368250 10.1101/gr.397002
66. Medvedovic M Sivaganesan S Bayesian infinite mixture model based clustering of gene expression profiles Bioinformatics (Oxford, England) 2002, 18(9):1194-1206. 10.1093/bioinformatics/18.9.1194 12217911
67. Dudoit S Fridlyand J Speed TP Comparison of discrimination methods for the classification of tumors using gene expression data Journal of the American Statistical Association 2002, 97(457):77-87. 10.1198/ 016214502753479248
68. Ramaswamy S Tamayo P Rifkin R Mukherjee S Yeang CH Angelo M Ladd C Reich M Latulippe E Mesirov JP et al. Multiclass cancer diagnosis using tumor gene expression signatures Proceedings of the National Academy of Sciences of the United States of America 2001, 98(26):15149-15154. 64998 11742071 10.1073/pnas.211566398
69. Venables WN Ripley BD Modern Applied Statistics with S New York: Springer 2002