Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data

BMC Medical Genomics

Volumn 6, Issue SUPPL.1, 2013, Pages

  Teng, Shaolei ^a   Yang, Jack Y ^b   Wang, Liangjiang ^a,c  

^a CLEMSON UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c GREENWOOD GENETIC CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE IDENTIFICATION; GENE TARGETING; GENETIC ANALYSIS; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RANDOM FOREST; SUPPORT VECTOR MACHINE;

BRAIN; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION; GENOME, HUMAN; HUMANS; LIVER; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; ROC CURVE; SEQUENCE ANALYSIS, DNA; SUPPORT VECTOR MACHINES;

EID: 84872969916     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-6-S1-S10     Document Type: Article

References (46)

1. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S, Proc Natl Acad Sci USA 2008 105 52 20870 20875 10.1073/pnas.0810772105 19104045
2. Insulin signalling and the regulation of glucose and lipid metabolism. Saltiel AR, Kahn CR, Nature 2001 414 6865 799 806 10.1038/414799a 11742412 (Pubitemid 34000783)
3. The microenvironment of the tumour-host interface. Liotta LA, Kohn EC, Nature 2001 411 6835 375 379 10.1038/35077241 11357145 (Pubitemid 32467047)
4. The human disease network. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL, Proc Natl Acad Sci USA 2007 104 21 8685 8690 10.1073/pnas. 0701361104 17502601 (Pubitemid 47175372)
5. Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure. Kadota K, Nishimura S, Bono H, Nakamura S, Hayashizaki Y, Okazaki Y, Takahashi K, Physiol Genomics 2003 12 3 251 259 12499447 (Pubitemid 37139704)
6. ROKU: a novel method for identification of tissue-specific genes. Kadota K, Ye J, Nakai Y, Terada T, Shimizu K, BMC Bioinformatics 2006 7 294 10.1186/1471-2105-7-294 16764735 (Pubitemid 44057307)
7. Detecting and profiling tissue-selective genes. Liang S, Li Y, Be X, Howes S, Liu W, Physiol Genomics 2006 26 2 158 162 10.1152/physiolgenomics. 00313.2005 16684803 (Pubitemid 44061325)
8. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG, PLoS Comput Biol 2009 5 6 1000417 10.1371/journal.pcbi.1000417 19543383
9. Microarray data integration for genome-wide analysis of human tissue-selective gene expression. Wang L, Srivastava AK, Schwartz CE, BMC Genomics 2010 11 Suppl 2 15 10.1186/1471-2164-11-S2-S15 21143798
10. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Li C, Hung Wong W, Genome Biol 2001 2 8 ESEARCH0032 11532216
11. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Li C, Wong WH, Proc Natl Acad Sci USA 2001 98 1 31 36 10.1073/pnas.98.1.31 11134512 (Pubitemid 32095858)
12. Classification and Regression by randomForest. Liaw A, Wiener M, R News 2002 2 3 18 22
13. What is a support vector machine? Noble WS, Nat Biotechnol 2006 24 12 1565 1567 10.1038/nbt1206-1565 17160063 (Pubitemid 44967481)
14. Learning to classify text using support vector machines. Joachims T, Boston: Kluwer Academic Publishers 2002
15. Measuring the accuracy of diagnostic systems. Swets JA, Science 1988 240 4857 1285 1293 10.1126/science.3287615 3287615
16. The use of the area under the ROC curve in the evaluation of machine learning algorithms. Bradley A, Pattern Recognition 1997 30 1145 1159 10.1016/S0031-3203(96)00142-2 (Pubitemid 127406521)
17. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA, Genome Biol 2003 4 5 3 10.1186/gb-2003-4-5-p3 12734009
18. SCOPE: a web server for practical de novo motif discovery. Carlson JM, Chakravarty A, DeZiel CE, Gross RH, Nucleic Acids Res 2007 35 Web Server 259 264 10.1093/nar/gkm310 17485471
19. DiRE: identifying distant regulatory elements of co-expressed genes. Gotea V, Ovcharenko I, Nucleic Acids Res 2008 36 Web Server 133 139 10.1093/nar/gkn300 18487623
20. TM4 microarray software suite. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J, Methods Enzymol 2006 411 134 193 16939790
21. A CNS-specific POU transcription factor, Brn-2, is required for establishing mammalian neural cell lineages. Fujii H, Hamada H, Neuron 1993 11 6 1197 1206 10.1016/0896-6273(93)90231-F 8274283 (Pubitemid 24015292)
22. Mutant huntingtin fragment selectively suppresses Brn-2 POU domain transcription factor to mediate hypothalamic cell dysfunction. Yamanaka T, Tosaki A, Miyazaki H, Kurosawa M, Furukawa Y, Yamada M, Nukina N, Hum Mol Genet 2010 19 11 2099 2112 10.1093/hmg/ddq087 20185558
23. The role of brain-derived neurotrophic factor (BDNF)-induced XBP1 splicing during brain development. Hayashi A, Kasahara T, Iwamoto K, Ishiwata M, Kametani M, Kakiuchi C, Furuichi T, Kato T, J Biol Chem 2007 282 47 34525 34534 10.1074/jbc.M704300200 17890727 (Pubitemid 350159475)
24. The transcription factor regulatory factor X1 increases the expression of neuronal glutamate transporter type 3. Ma K, Zheng S, Zuo Z, J Biol Chem 2006 281 30 21250 21255 10.1074/jbc.M600521200 16723357 (Pubitemid 44115464)
25. The non-apoptotic role of p53 in neuronal biology: enlightening the dark side of the moon. Tedeschi A, Di Giovanni S, EMBO Rep 2009 10 6 576 583 10.1038/embor.2009.89 19424293
26. Novel role for RNA-binding protein CUGBP2 in mammalian RNA editing. CUGBP2 modulates C to U editing of apolipoprotein B mRNA by interacting with apobec-1 and ACF, the apobec-1 complementation factor. Anant S, Henderson JO, Mukhopadhyay D, Navaratnam N, Kennedy S, Min J, Davidson NO, J Biol Chem 2001 276 50 47338 47351 10.1074/jbc.M104911200 11577082
27. Coupled mRNA stabilization and translational silencing of cyclooxygenase-2 by a novel RNA binding protein, CUGBP2. Mukhopadhyay D, Houchen CW, Kennedy S, Dieckgraefe BK, Anant S, Mol Cell 2003 11 1 113 126 10.1016/S1097-2765(03)00012-1 12535526 (Pubitemid 36126595)
28. Complex seizure disorder caused by Brunol4 deficiency in mice. Yang Y, Mahaffey CL, Berube N, Maddatu TP, Cox GA, Frankel WN, PLoS Genet 2007 3 7 124 10.1371/journal.pgen.0030124 17677002 (Pubitemid 47203977)
29. Amyloid-beta protein precursor (AbetaPP) intracellular domain-associated protein-1 proteins bind to AbetaPP and modulate its processing in an isoform-specific manner. Ghersi E, Noviello C, D'Adamio L, J Biol Chem 2004 279 47 49105 49112 10.1074/jbc.M405329200 15347684 (Pubitemid 39625793)
30. TRIM9, a novel brain-specific E3 ubiquitin ligase, is repressed in the brain of Parkinson's disease and dementia with Lewy bodies. Tanji K, Kamitani T, Mori F, Kakita A, Takahashi H, Wakabayashi K, Neurobiol Dis 2010 38 2 210 218 10.1016/j.nbd.2010.01.007 20085810
31. Cloning and primary structure of neurocan, a developmentally regulated, aggregating chondroitin sulfate proteoglycan of brain. Rauch U, Karthikeyan L, Maurel P, Margolis RU, Margolis RK, J Biol Chem 1992 267 27 19536 19547 1326557
32. LFG: an anti-apoptotic gene that provides protection from Fas-mediated cell death. Somia NV, Schmitt MJ, Vetter DE, Van Antwerp D, Heinemann SF, Verma IM, Proc Natl Acad Sci USA 1999 96 22 12667 12672 10.1073/pnas.96.22.12667 10535980 (Pubitemid 29513560)
33. Expression of cellular adhesion molecule 'OPCML' is down-regulated in gliomas and other brain tumours. Reed JE, Dunn JR, du Plessis DG, Shaw EJ, Reeves P, Gee AL, Warnke PC, Sellar GC, Moss DJ, Walker C, Neuropathol Appl Neurobiol 2007 33 1 77 85 17239010 (Pubitemid 46090312)
34. Identification of FXYD protein genes in a teleost: tissue-specific expression and response to salinity change. Tipsmark CK, Am J Physiol Regul Integr Comp Physiol 2008 294 4 1367 1378 10.1152/ajpregu.00454.2007 18256141 (Pubitemid 351490659)
35. Gnao1 (G alphaO protein) is a likely genetic contributor to variation in physical dependence on opioids in mice. Kest B, Smith SB, Schorscher-Petcu A, Austin JS, Ritchie J, Klein G, Rossi GC, Fortin A, Mogil JS, Neuroscience 2009 162 4 1255 1264 10.1016/j.neuroscience.2009.05.027 19460419
36. Localization of the synapsin II (SYN2) gene to human chromosome 3 and mouse chromosome 6. Li L, Chin LS, Greengard P, Copeland NG, Gilbert DJ, Jenkins NA, Genomics 1995 28 2 365 366 10.1006/geno.1995.1162 8530057
37. Synaptic vesicle protein 2, a new neuroendocrine cell marker. Portela-Gomes GM, Lukinius A, Grimelius L, Am J Pathol 2000 157 4 1299 1309 10.1016/S0002-9440(10)64645-7 11021834
38. Association study of neurotrophic tyrosine kinase receptor type 2 (NTRK2) and childhood-onset mood disorders. Adams JH, Wigg KG, King N, Burcescu I, Vetro A, Kiss E, Baji I, George CJ, Kennedy JL, Kovacs M, et al. Am J Med Genet B Neuropsychiatr Genet 2005 132B 1 90 95 10.1002/ajmg.b.30084 15389758 (Pubitemid 40066203)
39. Drosophila heparan sulfate 6-O-sulfotransferase (dHS6ST) gene. Structure, expression, and function in the formation of the tracheal system. Kamimura K, Fujise M, Villa F, Izumi S, Habuchi H, Kimata K, Nakato H, J Biol Chem 2001 276 20 17014 17021 10.1074/jbc.M011354200 11278892
40. A missense mutation of the Na+ channel alpha II subunit gene Na(v)1.2 in a patient with febrile and afebrile seizures causes channel dysfunction. Sugawara T, Tsurubuchi Y, Agarwala KL, Ito M, Fukuma G, Mazaki-Miyazaki E, Nagafuji H, Noda M, Imoto K, Wada K, et al. Proc Natl Acad Sci USA 2001 98 11 6384 6389 10.1073/pnas.111065098 11371648 (Pubitemid 32488246)
41. Liver in sepsis and systemic inflammatory response syndrome. Szabo G, Romics L Jr, Frendl G, Clin Liver Dis 2002 6 4 1045 1066 x 10.1016/S1089- 3261(02)00058-2 12516206 (Pubitemid 36026462)
42. Liver-enriched transcription factors in liver function and development. Part I: the hepatocyte nuclear factor network and liver-specific gene expression. Schrem H, Klempnauer J, Borlak J, Pharmacol Rev 2002 54 1 129 158 10.1124/pr.54.1.129 11870262 (Pubitemid 34208830)
43. The regulation of clotting factors. Kalafatis M, Egan JO, van't Veer C, Cawthern KM, Mann KG, Crit Rev Eukaryot Gene Expr 1997 7 3 241 280 10.1615/CritRevEukarGeneExpr.v7.i3.40 9399073 (Pubitemid 28101329)
44. Apoa-Ii directs morphogenetic movements of zebrafish embryo by preventing chromosome fusion during nuclear division in yolk syncytial layer. Zhang T, Yao S, Wang P, Yin C, Xiao C, Qian M, Liu D, Zheng L, Meng W, Zhu H, et al. J Biol Chem 2011
45. Genomic organization of a human 5beta-reductase and its pseudogene and substrate selectivity of the expressed enzyme. Charbonneau A, The VL, Biochim Biophys Acta 2001 1517 2 228 235 10.1016/S0167-4781(00)00278-5 11342103 (Pubitemid 32126520)
46. Comparative analyses of disease risk genes belonging to the acyl-CoA synthetase medium-chain (ACSM) family in human liver and cell lines. Boomgaarden I, Vock C, Klapper M, Doring F, Biochem Genet 2009 47 9-10 739 748 10.1007/s10528-009-9273-z 19634011