Glycotranscriptomics

Handbook of Glycomics

Volumn , Issue , 2010, Pages 95-135

  Nairn, Alison ^a   Moremen, Kelley ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882515947     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-373600-0.00005-6     Document Type: Chapter

References (254)

1. Varki A Biological roles of oligosaccharides: all of the theories are correct. Glycobiology 1993, 3:97-130.
2. Brockhausen I, Schutzbach J, Kuhns W Glycoproteins and their relationship to human disease. Acta Anat (Basel) 1998, 161:36-78.
3. Dennis JW, Granovsky M, Warren CE Protein glycosylation in development and disease. Bioessays 1999, 21:412-421.
4. Haltiwanger RS, Lowe JB Role of glycosylation in development. Annu Rev Biochem 2004, 73:491-537.
5. Taniguchi N, Miyoshi E, Gu J, Honke K, Matsumoto A Decoding sugar functions by identifying target glycoproteins. Curr Opin Struct Biol 2006, 16:561-566.
6. Marth JD Will the transgenic mouse serve as a Rosetta Stone to glycoconjugate function?. Glycoconj J 1994, 11:3-8.
7. Kornfeld R, Kornfeld S Assembly of asparagine-linked oligosaccharides. Annu Rev Biochem 1985, 54:631-664.
8. Schachter H Glycoproteins: their structure, biosynthesis and possible clinical implications. Clin Biochem 1984, 17:3-14.
9. Schachter H Coordination between enzyme specificity and intracellular compartmentation in the control of protein-bound oligosaccharide biosynthesis. Biol Cell 1984, 51:133-145.
10. Schachter H The "yellow brick road" to branched complex N-glycans. Glycobiology 1991, 1:453-461.
11. Handbook of Glycosyltransferases and Related Genes 2002, 670. Springer-Verlag, Tokyo. N. Taniguchi, K. Honke, M. Fukuda (Eds.).
12. Nairn AV, York WS, Harris K, Hall EM, Pierce JM, Moremen KW Regulation of glycan structures in animal tissues: Transcript profiling of glycan-related genes. J Biol Chem 2008, 283:17298-17313.
13. Comelli EM, Head SR, Gilmartin T, Whisenant T, Haslam SM, North SJ, Wong N-K, Kudo T, Narimatsu H, Esko JD, Drickamer K, Dell A, Paulson JC A focused microarray approach to functional glycomics: transcriptional regulation of the glycome. Glycobiology 2006, 16:117-131.
14. Nairn AV, Kinoshita-Toyoda A, Toyoda H, Xie J, Harris K, Dalton S, Kulik M, Pierce JM, Toida T, Moremen KW, Linhardt RJ Glycomics of proteoglycan biosynthesis in murine embryonic stem cell differentiation. J Proteome Res 2007, 6:4374-4387.
15. Aoki K, Perlman M, Lim JM, Cantu R, Wells L, Tiemeyer M Dynamic developmental elaboration of N-linked glycan complexity in the Drosophila melanogaster embryo. J Biol Chem 2007, 282:9127-9142.
16. Kui Wong N, Easton RL, Panico M, Sutton-Smith M, Morrison JC, Lattanzio FA, Morris HR, Clark GF, Dell A, Patankar MS Characterization of the oligosaccharides associated with the human ovarian tumor marker CA125. J Biol Chem 2003, 278:28619-28634.
17. Sutton-Smith M, Morris HR, Grewal PK, Hewitt JE, Bittner RE, Goldin E, Schiffmann R, Dell A MS screening strategies: investigating the glycomes of knockout and myodystrophic mice and leukodystrophic human brains. Biochem Soc Symp 2002, 69:105-115.
18. Bax M, Garcia-Vallejo JJ, Jang-Lee J, North SJ, Gilmartin TJ, Hernandez G, Crocker PR, Leffler H, Head SR, Haslam SM, Dell A, van Kooyk Y Dendritic cell maturation results in pronounced changes in glycan expression affecting recognition by siglecs and galectins. J Immunol 2007, 179:8216-8224.
19. Hemmoranta H, Satomaa T, Blomqvist M, Heiskanen A, Aitio O, Saarinen J, Natunen J, Partanen J, Laine J, Jaatinen T N-glycan structures and associated gene expression reflect the characteristic N-glycosylation pattern of human hematopoietic stem and progenitor cells. Exp Hematol 2007, 35:1279-1292.
20. Naito Y, Takematsu H, Koyama S, Miyake S, Yamamoto H, Fujinawa R, Sugai M, Okuno Y, Tsujimoto G, Yamaji T, Hashimoto Y, Itohara S, Kawasaki T, Suzuki A, Kozutsumi Y Germinal center marker GL7 probes activation-dependent repression of N-glycolylneuraminic acid, a sialic acid species involved in the negative modulation of B-cell activation. Mol Cell Biol 2007, 27:3008-3022.
21. Smith FI, Qu Q, Hong SJ, Kim KS, Gilmartin TJ, Head SR Gene expression profiling of mouse postnatal cerebellar development using oligonucleotide microarrays designed to detect differences in glycoconjugate expression. Gene Expr Patterns 2005, 5:740-749.
22. Yamamoto H, Takematsu H, Fujinawa R, Naito Y, Okuno Y, Tsujimoto G, Suzuki A, Kozutsumi Y Correlation Index-Based Responsible-Enzyme Gene Screening (CIRES), a novel DNA microarray-based method for enzyme gene involved in glycan biosynthesis. PLoS ONE 2007, 2:e1232.
23. Young WW, Holcomb DR, Ten Hagen KG, Tabak LA. Expression of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase isoforms in murine tissues determined by real-time PCR: a new view of a large family. Glycobiology 2003, 13:549-557.
24. Ishii A, Ikeda T, Hitoshi S, Fujimoto I, Torii T, Sakuma K, Nakakita S, Hase S, Ikenaka K Developmental changes in the expression of glycogenes and the content of N-glycans in the mouse cerebral cortex. Glycobiology 2007, 17:261-276.
25. Coutinho PM, Deleury E, Davies GJ, Henrissat B An evolving hierarchical family classification for glycosyltransferases. J Mol Biol 2003, 328:307-317.
26. Coutinho PM, Henrissat B Carbohydrate-active enzymes: an integrated database approach. Recent advances in carbohydrate bioengineering 1999, 3-12. The Royal Society of Chemistry, Cambridge. G. Davies, H.J. Gilbert, B. Henrissat, B. Svensson (Eds.).
27. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y KEGG for linking genomes to life and the environment. Nucleic Acids Res 2007, 36:D480-D484.
28. Kanehisa M, Goto S KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
29. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-D357.
30. Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res 2003, 31:219-223.
31. Garcia-Vallejo JJ, Gringhuis SI, van Dijk W, van Die I Gene expression analysis of glycosylation-related genes by real-time polymerase chain reaction. Methods Mol Biol 2006, 347:187-209.
32. Garcia-Vallejo JJ, Van Dijk W, Van Het Hof B, Van Die I, Engelse MA, Van Hinsbergh VW, Gringhuis SI Activation of human endothelial cells by tumor necrosis factor-alpha results in profound changes in the expression of glycosylation-related genes. J Cell Physiol 2006, 206:203-210.
33. Essentials of Glycobiology 2008, Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY. 2nd edn. A. Varki, R.D. Cummings, J.D. Esko, H.H. Freeze, P. Stanley, C.R. Bertozzi, G.W. Hart, M.E. Etzler (Eds.).
34. Hediger MA, Rhoads DB Molecular physiology of sodium-glucose cotransporters. Physiol Rev 1994, 74:993-1026.
35. Wood IS, Trayhurn P Glucose transporters (GLUT and SGLT): expanded families of sugar transport proteins. Br J Nutr 2003, 89:3-9.
36. Thorens B Glucose transporters in the regulation of intestinal, renal, and liver glucose fluxes. Am J Physiol 1996, 270:G541-G553.
37. Bell GI, Burant CF, Takeda J, Gould GW Structure and function of mammalian facilitative sugar transporters. J Biol Chem 1993, 268:19161-19164.
38. Mueckler M, Caruso C, Baldwin SA, Panico M, Blench I, Morris HR, Allard WJ, Lienhard GE, Lodish HF Sequence and structure of a human glucose transporter. Science 1985, 229:941-945.
39. Henderson PJ The 12-transmembrane helix transporters. Curr Opin Cell Biol 1993, 5:708-721.
40. Joost HG, Thorens B The extended GLUT-family of sugar/polyol transport facilitators: nomenclature, sequence characteristics, and potential function of its novel members (review). Mol Membr Biol 2001, 18:247-256.
41. Watson RT, Pessin JE Subcellular compartmentalization and trafficking of the insulin-responsive glucose transporter, GLUT4. Exp Cell Res 2001, 271:75-83.
42. Panneerselvam K, Freeze HH Mannose enters mammalian cells using a specific transporter that is insensitive to glucose. J Biol Chem 1996, 271:9417-9421.
43. Leck JR, Wiese TJ Purification and characterization of the L-fucose transporter. Protein Expr Purif 2004, 37:288-293.
44. Cardenas ML, Cornish-Bowden A, Ureta T Evolution and regulatory role of the hexokinases. Biochim Biophys Acta 1998, 1401:242-264.
45. Munster AK, Eckhardt M, Potvin B, Muhlenhoff M, Stanley P, Gerardy-Schahn R Mammalian cytidine 5'-monophosphate N-acetylneuraminic acid synthetase: a nuclear protein with evolutionarily conserved structural motifs. Proc Natl Acad Sci USA 1998, 95:9140-9145.
46. Hirschberg CB, Robbins PW, Abeijon C Transporters of nucleotide sugars, ATP, and nucleotide sulfate in the endoplasmic reticulum and Golgi apparatus. Annu Rev Biochem 1998, 67:49-69.
47. Munster AK, Weinhold B, Gotza B, Muhlenhoff M, Frosch M, Gerardy-Schahn R Nuclear localization signal of murine CMP-Neu5Ac synthetase includes residues required for both nuclear targeting and enzymatic activity. J Biol Chem 2002, 277:19688-19696.
48. Helenius A, Aebi M Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem 2004, 73:1019-1049.
49. Tiede A, Bastisch I, Schubert J, Orlean P, Schmidt RE Biosynthesis of glycosylphosphatidylinositols in mammals and unicellular microbes. Biol Chem 1999, 380:503-523.
50. Vosseller K, Wells L, Hart GW Nucleocytoplasmic O-glycosylation: O-GlcNAc and functional proteomics. Biochimie 2001, 83:575-581.
51. Weigel PH, DeAngelis PL Hyaluronan synthases: a decade-plus of novel glycosyltransferases. J Biol Chem 2007, 282:36777-36781.
52. Orlean P Enzymes that recognize dolichols participate in three glycosylation pathways and are required for protein secretion. Biochem Cell Biol 1992, 70:438-447.
53. Herscovics A, Orlean P Glycoprotein biosynthesis in yeast. FASEB J 1993, 7:540-550.
54. Saier MH, Tran CV, Barabote RD. TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res 2006, 34:D181-D186.
55. Gao XD, Nishikawa A, Dean N Physical interactions between the Alg1, Alg2, and Alg11 mannosyltransferases of the endoplasmic reticulum. Glycobiology 2004, 14:559-570.
56. Moremen K a-Mannosidases in Asparagine-linked oligosaccharide processing and catabolism. Oligosaccharides in Chemistry and Biology: A Comprehensive Handbook 2000, vol. II:81-117. Wiley and Sons, Inc., New York, NY, Biology of Saccharides, Part 1: Biosynthesis of Glycoconjugates. B. Ernst, G. Hart, P. Sinay (Eds.).
57. Moremen KW, Trimble RB, Herscovics A Glycosidases of the asparagine-linked oligosaccharide processing pathway. Glycobiology 1994, 4:113-125.
58. Wu Y, Swulius MT, Moremen KW, Sifers RN Elucidation of the molecular logic by which misfolded alpha 1-antitrypsin is preferentially selected for degradation. Proc Natl Acad Sci USA 2003, 100:8229-8234.
59. Schachter H The joys of HexNAc. The synthesis and function of N- and O-glycan branches. Glycoconj J 2000, 17:465-483.
60. Spiro RG Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 2002, 12:43R-56R.
61. Hanisch FG O-glycosylation of the mucin type. Biol Chem 2001, 382:143-149.
62. Ten Hagen KG, Fritz TA, Tabak LA All in the family: the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases. Glycobiology 2003, 13:1R-16R.
63. Esko JD, Selleck SB Order out of chaos: assembly of ligand binding sites in heparan sulfate. Annu Rev Biochem 2002, 71:435-471.
64. Wilson IB The never-ending story of peptide O-xylosyltransferase. Cell Mol Life Sci 2004, 61:794-809.
65. Taylor KR, Gallo RL Glycosaminoglycans and their proteoglycans: host-associated molecular patterns for initiation and modulation of inflammation. FASEB J 2006, 20:9-22.
66. Busse M, Feta A, Presto J, Wilen M, Gronning M, Kjellen L, Kusche-Gullberg M Contribution of EXT1, EXT2, and EXTL3 to heparan sulfate chain elongation. J Biol Chem 2007, 282:32802-32810.
67. Izumikawa T, Koike T, Shiozawa S, Sugahara K, Tamura J, Kitagawa H Identification of chondroitin sulfate glucuronyltransferase as chondroitin synthase-3 involved in chondroitin polymerization: chondroitin polymerization is achieved by multiple enzyme complexes consisting of chondroitin synthase family members. J Biol Chem 2008, 283:11396-113406.
68. Sugahara K, Kitagawa H Heparin and heparan sulfate biosynthesis. IUBMB Life 2002, 54:163-175.
69. Silbert JE, Sugumaran G Biosynthesis of chondroitin/dermatan sulfate. IUBMB Life 2002, 54:177-186.
70. Itano N, Kimata K Mammalian hyaluronan synthases. IUBMB Life 2002, 54:195-199.
71. Okajima T, Matsuura A, Matsuda T Biological functions of glycosyltransferase genes involved in O-fucose glycan synthesis. J Biochem 2008, 144:1-6.
72. Panin VM, Shao L, Lei L, Moloney DJ, Irvine KD, Haltiwanger RS Notch ligands are substrates for protein O-fucosyltransferase-1 and Fringe. J Biol Chem 2002, 277:29945-29952.
73. Haines N, Irvine KD Glycosylation regulates Notch signalling. Nat Rev Mol Cell Biol 2003, 4:786-797.
74. Shao L, Moloney DJ, Haltiwanger R Fringe modifies O-fucose on mouse Notch1 at epidermal growth factor-like repeats within the ligand-binding site and the Abruptex region. J Biol Chem 2003, 278:7775-7782.
75. Shao L, Haltiwanger RS O-fucose modifications of epidermal growth factor-like repeats and thrombospondin type 1 repeats: unusual modifications in unusual places. Cell Mol Life Sci 2003, 60:241-250.
76. Stanley P Regulation of Notch signaling by glycosylation. Curr Opin Struct Biol 2007, 17:530-535.
77. Shi S, Ge C, Luo Y, Hou X, Haltiwanger RS, Stanley P The threonine that carries fucose, but not fucose, is required for Cripto to facilitate Nodal signaling. J Biol Chem 2007, 282:20133-20141.
78. Stanley P Glucose: a novel regulator of notch signaling. ACS Chem Biol 2008, 3:210-213.
79. Nishimura H, Yamashita S, Zeng Z, Walz DA, Iwanaga S Evidence for the existence of O-linked sugar chains consisting of glucose and xylose in bovine thrombospondin. J Biochem 1992, 111:460-464.
80. Loriol C, Dupuy F, Rampal R, Dlugosz MA, Haltiwanger RS, Maftah A, Germot A Molecular evolution of protein O-fucosyltransferase genes and splice variants. Glycobiology 2006, 16:736-747.
81. Luo Y, Koles K, Vorndam W, Haltiwanger RS, Panin VM Protein O-fucosyltransferase 2 adds O-fucose to thrombospondin type 1 repeats. J Biol Chem 2006, 281:9393-9399.
82. Luo Y, Nita-Lazar A, Haltiwanger RS Two distinct pathways for O-fucosylation of epidermal growth factor-like or thrombospondin type 1 repeats. J Biol Chem 2006, 281:9385-9392.
83. Sato T, Sato M, Kiyohara K, Sogabe M, Shikanai T, Kikuchi N, Togayachi A, Ishida H, Ito H, Kameyama A, Gotoh M, Narimatsu H Molecular cloning and characterization of a novel human beta1,3-glucosyltransferase, which is localized at the endoplasmic reticulum and glucosylates O-linked fucosylglycan on thrombospondin type 1 repeat domain. Glycobiology 2006, 16:1194-1206.
84. Chiba A, Matsumura K, Yamada H, Inazu T, Shimizu T, Kusunoki S, Kanazawa I, Kobata A, Endo T Structures of sialylated O-linked oligosaccharides of bovine peripheral nerve alpha-dystroglycan. The role of a novel O-mannosyl-type oligosaccharide in the binding of alpha-dystroglycan with laminin. J Biol Chem 1997, 272:2156-2162.
85. Barresi R, Campbell KP Dystroglycan: from biosynthesis to pathogenesis of human disease. J Cell Sci 2006, 119:199-207.
86. Manya H, Chiba A, Yoshida A, Wang X, Chiba Y, Jigami Y, Margolis RU, Endo T Demonstration of mammalian protein O-mannosyltransferase activity: coexpression of POMT1 and POMT2 required for enzymatic activity. Proc Natl Acad Sci USA 2004, 101:500-505.
87. Manya H, Sakai K, Kobayashi K, Taniguchi K, Kawakita M, Toda T, Endo T Loss-of-function of an N-acetylglucosaminyltransferase, POMGnT1, in muscle-eye-brain disease. Biochem Biophys Res Commun 2003, 306:93-97.
88. Jimenez-Mallebrera C, Torelli S, Feng L, Kim J, Godfrey C, Clement E, Mein R, Abbs S, Brown SC, Campbell KP, Kroger S, Talim B, Topaloglu H, Quinlivan R, Roper H, Childs AM, Kinali M, Sewry CA, Muntoni F. A comparative study of alpha-dystroglycan glycosylation in dystroglycanopathies suggests that the hypoglycosylation of alpha-dystroglycan does not consistently correlate with clinical severity. Brain Pathol 2008.
89. Godfrey C, Clement E, Mein R, Brockington M, Smith J, Talim B, Straub V, Robb S, Quinlivan R, Feng L, Jimenez-Mallebrera C, Mercuri E, Manzur AY, Kinali M, Torelli S, Brown SC, Sewry CA, Bushby K, Topaloglu H, North K, Abbs S, Muntoni F Refining genotype phenotype correlations in muscular dystrophies with defective glycosylation of dystroglycan. Brain 2007, 130:2725-2735.
90. Lahiri S, Futerman AH The metabolism and function of sphingolipids and glycosphingolipids. Cell Mol Life Sci 2007, 64:2270-2284.
91. Sandhoff K, Kolter T Biosynthesis and degradation of mammalian glycosphingolipids. Philos Trans R Soc Lond B Biol Sci 2003, 358:847-861.
92. Furukawa K Recent progress in the analysis of gangliosides biosynthesis. Nagoya J Med Sci 1998, 61:27-35.
93. Chatterjee S, Pandey A The Yin and Yang of lactosylceramide metabolism: implications in cell function. Biochim Biophys Acta 2008, 1780:370-382.
94. Orlean P, Menon AK Thematic review series: lipid posttranslational modifications. GPI anchoring of protein in yeast and mammalian cells, or: how we learned to stop worrying and love glycophospholipids. J Lipid Res 2007, 48:993-1011.
95. Lomako J, Lomako WM, Whelan WJ Glycogenin: the primer for mammalian and yeast glycogen synthesis. Biochim Biophys Acta 2004, 1673:45-55.
96. Hurley TD, Stout S, Miner E, Zhou J, Roach PJ Requirements for catalysis in mammalian glycogenin. J Biol Chem 2005, 280:23892-23899.
97. Browner MF, Nakano K, Bang AG, Fletterick RJ Human muscle glycogen synthase cDNA sequence: a negatively charged protein with an asymmetric charge distribution. Proc Natl Acad Sci USA 1989, 86:1443-1447.
98. Westphal SA, Nuttall FQ Comparative characterization of human and rat liver glycogen synthase. Arch Biochem Biophys 1992, 292:479-486.
99. Greenberg CC, Jurczak MJ, Danos AM, Brady MJ Glycogen branches out: new perspectives on the role of glycogen metabolism in the integration of metabolic pathways. Am J Physiol Endocrinol Metab 2006, 291:E1-E8.
100. Matsuishi T, Yoshino M, Terasawa K, Nonaka I Childhood acid maltase deficiency. A clinical, biochemical, and morphologic study of three patients. Arch Neurol 1984, 41:47-52.
101. Roth J Protein glycosylation in the endoplasmic reticulum and the Golgi apparatus and cell type-specificity of cell surface glycoconjugate expression: analysis by the protein A-gold and lectin-gold techniques. Histochem Cell Biol 1996, 106:79-92.
102. Young RA, Davis RW Efficient isolation of genes by using antibody probes. Proc Natl Acad Sci USA 1983, 80:1194-1198.
103. Shaper NL, Shaper JH, Meuth JL, Fox JL, Chang H, Kirsch IR, Hollis GF Bovine galactosyltransferase: identification of a clone by direct immunological screening of a cDNA expression library. Proc Natl Acad Sci USA 1986, 83:1573-1577.
104. Weinstein J, Lee EU, McEntee K, Lai PH, Paulson JC Primary structure of beta-galactoside alpha 2,6-sialyltransferase. Conversion of membrane-bound enzyme to soluble forms by cleavage of the NH2-terminal signal anchor. J Biol Chem 1987, 262:17735-17743.
105. Joziasse DH, Shaper JH, Van den Eijnden DH, Van Tunen AJ, Shaper NL Bovine alpha 1→3-galactosyltransferase: isolation and characterization of a cDNA clone. Identification of homologous sequences in human genomic DNA. J Biol Chem 1989, 264:14290-14297.
106. Narimatsu H, Sinha S, Brew K, Okayama H, Qasba PK Cloning and sequencing of cDNA of bovine N-acetylglucosamine (beta 1-4)galactosyltransferase. Proc Natl Acad Sci USA 1986, 83:4720-4724.
107. Appert HE, Rutherford TJ, Tarr GE, Wiest JS, Thomford NR, McCorquodale DJ Isolation of a cDNA coding for human galactosyltransferase. Biochem Biophys Res Commun 1986, 139:163-168.
108. Frohman MA, Dush MK, Martin GR Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci USA 1988, 85:8998-9002.
109. Lee CC, Wu XW, Gibbs RA, Cook RG, Muzny DM, Caskey CT Generation of cDNA probes directed by amino acid sequence: cloning of urate oxidase. Science 1988, 239:1288-1291.
110. Moremen KW Isolation of a rat liver Golgi mannosidase II clone by mixed oligonucleotide-primed amplification of cDNA. Proc Natl Acad Sci USA 1989, 86:5276-5280.
111. Yamamoto F, Marken J, Tsuji T, White T, Clausen H, Hakomori S Cloning and characterization of DNA complementary to human UDP-GalNAc: Fuc alpha 1-2Gal alpha 1→3GalNAc transferase (histo-blood group A transferase) mRNA. J Biol Chem 1990, 265:1146-1151.
112. Sarkar M, Hull E, Nishikawa Y, Simpson RJ, Moritz RL, Dunn R, Schachter H Molecular cloning and expression of cDNA encoding the enzyme that controls conversion of high-mannose to hybrid and complex N-glycans: UDP-N-acetylglucosamine: alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I. Proc Natl Acad Sci USA 1991, 88:234-238.
113. Wen DX, Livingston BD, Medzihradszky KF, Kelm S, Burlingame AL, Paulson JC Primary structure of Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase determined by mass spectrometry sequence analysis and molecular cloning. Evidence for a protein motif in the sialyltransferase gene family. J Biol Chem 1992, 267:21011-21019.
114. Shoreibah M, Perng GS, Adler B, Weinstein J, Basu R, Cupples R, Wen D, Browne JK, Buckhaults P, Fregien N, Pierce M Isolation, characterization, and expression of a cDNA encoding N-acetylglucosaminyltransferase V. J Biol Chem 1993, 268:15381-15385.
115. Homa FL, Hollander T, Lehman DJ, Thomsen DR, Elhammer AP Isolation and expression of a cDNA clone encoding a bovine UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase. J Biol Chem 1993, 268:12609-12616.
116. White T, Bennett EP, Takio K, Sorensen T, Bonding N, Clausen H Purification and cDNA cloning of a human UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase. J Biol Chem 1995, 270:24156-24165.
117. D'Agostaro GA, Zingoni A, Moritz RL, Simpson RJ, Schachter H, Bendiak B Molecular cloning and expression of cDNA encoding the rat UDP-N-acetylglucosamine:alpha-6-D-mannoside beta-1,2-N-acetylglucosaminyltransferase II. J Biol Chem 1995, 270:15211-15221.
118. Lal A, Schutzbach JS, Forsee WT, Neame PJ, Moremen KW Isolation and expression of murine and rabbit cDNAs encoding an alpha 1,2-mannosidase involved in the processing of asparagine-linked oligosaccharides. J Biol Chem 1994, 269:9872-9881.
119. Ju T, Brewer K, D'Souza A, Cummings RD, Canfield WM Cloning and expression of human core 1 beta1,3-galactosyltransferase. J Biol Chem 2002, 277:178-186.
120. Herscovics A, Schneikert J, Athanassiadis A, Moremen KW Isolation of a mouse Golgi mannosidase cDNA, a member of a gene family conserved from yeast to mammals. J Biol Chem 1994, 269:9864-9871.
121. Gonzalez DS, Karaveg K, Vandersall-Nairn AS, Lal A, Moremen KW Identification, expression, and characterization of a cDNA encoding human endoplasmic reticulum mannosidase I, the enzyme that catalyzes the first mannose trimming step in mammalian Asn-linked oligosaccharide biosynthesis. J Biol Chem 1999, 274:21375-21386.
122. Livingston BD, Paulson JC Polymerase chain reaction cloning of a developmentally regulated member of the sialyltransferase gene family. J Biol Chem 1993, 268:11504-11507.
123. Kitagawa H, Paulson JC Cloning and expression of human Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase. Biochem Biophys Res Commun 1993, 194:375-382.
124. Kitagawa H, Paulson JC Differential expression of five sialyltransferase genes in human tissues. J Biol Chem 1994, 269:17872-17878.
125. Kitagawa H, Paulson JC Cloning of a novel alpha 2,3-sialyltransferase that sialylates glycoprotein and glycolipid carbohydrate groups. J Biol Chem 1994, 269:1394-1401.
126. Larsen RD, Rajan VP, Ruff MM, Kukowska-Latallo J, Cummings RD, Lowe JB Isolation of a cDNA encoding a murine UDPgalactose:beta-D-galactosyl- 1,4-N-acetyl-D-glucosaminide alpha-1,3-galactosyltransferase: expression cloning by gene transfer. Proc Natl Acad Sci USA 1989, 86:8227-8231.
127. Kukowska-Latallo JF, Larsen RD, Nair RP, Lowe JB A cloned human cDNA determines expression of a mouse stage-specific embryonic antigen and the Lewis blood group alpha(1,3/1,4)fucosyltransferase. Genes Dev 1990, 4:1288-1303.
128. Smith PL, Lowe JB Molecular cloning of a murine N-acetylgalactosamine transferase cDNA that determines expression of the T lymphocyte-specific CT oligosaccharide differentiation antigen. J Biol Chem 1994, 269:15162-15171.
129. Nagata Y, Yamashiro S, Yodoi J, Lloyd KO, Shiku H, Furukawa K Expression cloning of beta 1,4 N-acetylgalactosaminyltransferase cDNAs that determine the expression of GM2 and GD2 gangliosides. J Biol Chem 1992, 267:12082-12089.
130. Misago M, Liao YF, Kudo S, Eto S, Mattei MG, Moremen KW, Fukuda MN Molecular cloning and expression of cDNAs encoding human alpha-mannosidase II and a previously unrecognized alpha-mannosidase IIx isozyme. Proc Natl Acad Sci USA 1995, 92:11766-11770.
131. Lowe JB, Kukowska-Latallo JF, Nair RP, Larsen RD, Marks RM, Macher BA, Kelly RJ, Ernst LK Molecular cloning of a human fucosyltransferase gene that determines expression of the Lewis x and VIM-2 epitopes but not ELAM-1-dependent cell adhesion. J Biol Chem 1991, 266:17467-17477.
132. Weston BW, Smith PL, Kelly RJ, Lowe JB Molecular cloning of a fourth member of a human alpha (1,3)fucosyltransferase gene family. Multiple homologous sequences that determine expression of the Lewis x, sialyl Lewis x, and difucosyl sialyl Lewis x epitopes. J Biol Chem 1992, 267:24575-24584.
133. Weston BW, Nair RP, Larsen RD, Lowe JB Isolation of a novel human alpha (1,3)fucosyltransferase gene and molecular comparison to the human Lewis blood group alpha (1,3/1,4)fucosyltransferase gene. Syntenic, homologous, nonallelic genes encoding enzymes with distinct acceptor substrate specificities. J Biol Chem 1992, 267:4152-4160.
134. Natsuka S, Gersten KM, Zenita K, Kannagi R, Lowe JB Molecular cloning of a cDNA encoding a novel human leukocyte alpha-1,3-fucosyltransferase capable of synthesizing the sialyl Lewis x determinant. J Biol Chem 1994, 269:16789-16794.
135. Rouquier S, Lowe JB, Kelly RJ, Fertitta AL, Lennon GG, Giorgi D Molecular cloning of a human genomic region containing the H blood group alpha(1,2)fucosyltransferase gene and two H locus-related DNA restriction fragments. Isolation of a candidate for the human Secretor blood group locus. J Biol Chem 1995, 270:4632-4639.
136. Shaper NL, Hollis GF, Douglas JG, Kirsch IR, Shaper JH Characterization of the full length cDNA for murine beta-1,4-galactosyltransferase, Novel features at the, 5' -end predict two translational start sites at two in-frame AUGs. J Biol Chem 1988, 263:10420-10428.
137. Gersten KM, Natsuka S, Trinchera M, Petryniak B, Kelly RJ, Hiraiwa N, Jenkins NA, Gilbert DJ, Copeland NG, Lowe JB Molecular cloning, expression, chromosomal assignment, and tissue-specific expression of a murine alpha-(1,3)-fucosyltransferase locus corresponding to the human ELAM-1 ligand fucosyl transferase. J Biol Chem 1995, 270:25047-25056.
138. Domino SE, Zhang L, Lowe JB Molecular cloning, genomic mapping, and expression of two secretor blood group alpha (1,2)fucosyltransferase genes differentially regulated in mouse uterine epithelium and gastrointestinal tract. J Biol Chem 2001, 276:23748-23756.
139. Hennet T, Dinter A, Kuhnert P, Mattu TS, Rudd PM, Berger EG Genomic cloning and expression of three murine UDP-galactose: beta-N-acetylglucosamine beta1,3-galactosyltransferase genes. J Biol Chem 1998, 273:58-65.
140. Amado M, Almeida R, Carneiro F, Levery SB, Holmes EH, Nomoto M, Hollingsworth MA, Hassan H, Schwientek T, Nielsen PA, Bennett EP, Clausen H A family of human beta3-galactosyltransferases. Characterization of four members of a UDP-galactose:beta-N-acetyl-glucosamine/beta-nacetyl-galactosamine beta-1,3-galactosyltransferase family. J Biol Chem 1998, 273:12770-12778.
141. Park C, Meng L, Stanton LH, Collins RE, Mast SW, Yi X, Strachan H, Moremen KW Characterization of a human core-specific lysosomal {alpha}1,6-mannosidase involved in N-glycan catabolism. J Biol Chem 2005, 280:37204-37216.
142. Huffaker TC, Robbins PW Temperature-sensitive yeast mutants deficient in asparagine-linked glycosylation. J Biol Chem 1982, 257:3203-3210.
143. Huffaker TC, Robbins PW Yeast mutants deficient in protein glycosylation. Proc Natl Acad Sci USA 1983, 80:7466-7470.
144. Runge KW, Huffaker TC, Robbins PW Two yeast mutations in glucosylation steps of the asparagine glycosylation pathway. J Biol Chem 1984, 259:412-417.
145. Runge KW, Robbins PW A new yeast mutation in the glucosylation steps of the asparagine-linked glycosylation pathway. Formation of a novel asparagine-linked oligosaccharide containing two glucose residues. J Biol Chem 1986, 261:15582-15590.
146. Hirose S, Mohney RP, Mutka SC, Ravi L, Singleton DR, Perry G, Tartakoff AM, Medof ME Derivation and characterization of glycoinositol-phospholipid anchor-defective human K562 cell clones. J Biol Chem 1992, 267:5272-5278.
147. Mohney RP, Knez JJ, Ravi L, Sevlever D, Rosenberry TL, Hirose S, Medof ME Glycoinositol phospholipid anchor-defective K562 mutants with biochemical lesions distinct from those in Thy-1- murine lymphoma mutants. J Biol Chem 1994, 269:6536-6542.
148. Takahashi M, Inoue N, Ohishi K, Maeda Y, Nakamura N, Endo Y, Fujita T, Takeda J, Kinoshita T PIG-B, a membrane protein of the endoplasmic reticulum with a large lumenal domain, is involved in transferring the third mannose of the GPI anchor. EMBO J 1996, 15:4254-4261.
149. Takeda J, Kinoshita T GPI-anchor biosynthesis. Trends Biochem Sci 1995, 20:367-371.
150. Taylor ME, Drickamer K Introduction to Glycobiology 2006, Oxford University Press, Oxford. Second edn.
151. Kanehisa M, Goto S, Kawashima S, Nakaya A The KEGG databases at GenomeNet. Nucleic Acids Res 2002, 30:42-46.
152. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2007, 35:D5-D12.
153. Comelli EM, Amado M, Head SR, Paulson JC Custom microarray for glycobiologists: considerations for glycosyltransferase gene expression profiling. Biochem Soc Symp 2002, 69>:135-142.
154. Alwine JC, Kemp DJ, Stark GR Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci USA 1977, 74:5350-5354.
155. Sato T, Furukawa K, Bakker H, Van den Eijnden DH, Van Die I Molecular cloning of a human cDNA encoding beta-1,4-galactosyltransferase with 37% identity to mammalian UDP-Gal:GlcNAc beta-1,4-galactosyltransferase. Proc Natl Acad Sci USA 1998, 95:472-477.
156. Shaper NL, Wright WW, Shaper JH Murine beta 1,4-galactosyltransferase: both the amounts and structure of the mRNA are regulated during spermatogenesis. Proc Natl Acad Sci USA 1990, 87:791-795.
157. Takashima S, Ishida HK, Inazu T, Ando T, Ishida H, Kiso M, Tsuji S, Tsujimoto M Molecular cloning and expression of a sixth type of alpha 2,8-sialyltransferase (ST8Sia VI) that sialylates O-glycans. J Biol Chem 2002, 277:24030-24038.
158. Lo NW, Shaper JH, Pevsner J, Shaper NL The expanding beta 4-galactosyltransferase gene family: messages from the databanks. Glycobiology 1998, 8:517-526.
159. Lin B, Saito M, Sakakibara Y, Hayashi Y, Yanagisawa M, Iwamori M Characterization of three members of murine alpha 1,2-fucosyltransferases: Change in the expression of the Se gene in the intestine of mice after administration of microbes. Arch Biochem Biophys 2001, 388:207-215.
160. Nakamura N, Yamakawa N, Sato T, Tojo H, Tachi C, Furukawa K Differential gene expression of beta-1,4-galactosyltransferases I, II and V during
161. Granovsky M, Fode C, Warren CE, Campbell RM, Marth JD, Pierce M, Fregien N, Dennis JW GlcNAc-transferase V and core 2 GlcNAc-transferase expression in the developing mouse embryo. Glycobiology 1995, 5:797-806.
162. Yan M, Cheng C, Ding F, Jiang J, Gao L, Xia C, Shen A The expression patterns of beta1,4 galactosyltransferase I and V mRNAs, and Galbeta1-4GlcNAc group in rat gastrocnemius muscles post sciatic nerve injury. Glycoconj J 2008, 25:685-701.
163. Tremblay LO, Nagy Kovacs E, Daniels E, Wong NK, Sutton-Smith M, Morris HR, Dell A, Marcinkiewicz E, Seidah NG, McKerlie C, Herscovics A Respiratory distress and neonatal lethality in mice lacking Golgi alpha1,2-mannosidase IB involved in N-glycan maturation. J Biol Chem 2007, 282:2558-2566.
164. Chen SH, Zhou S, Tan J, Schachter H Transcriptional regulation of the human UDP-GlcNAc:alpha-6-D-mannoside beta-1-2-N-acetylglucosaminyltransferase II gene (MGAT2) which controls complex N-glycan synthesis. Glycoconj J 1998, 15:301-308.
165. O'Hanlon TP, Lau KM, Wang XC, Lau JT Tissue-specific expression of beta-galactoside alpha-2,6-sialyltransferase. Transcript heterogeneity predicts a divergent polypeptide. J Biol Chem 1989, 264:17389-17394.
166. Wang X, O'Hanlon TP, Young RF, Lau JT Rat beta-galactoside alpha 2,6-sialyltransferase genomic organization: alternate promoters direct the synthesis of liver and kidney transcripts. Glycobiology 1990, 1:25-31.
167. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996, 14:1675-1680.
168. Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A, Richmond T, Gorski T, Berg JP, Ballin J, McCormick M, Norton J, Pollock T, Sumwalt T, Butcher L, Porter D, Molla M, Hall C, Blattner F, Sussman MR, Wallace RL, Cerrina F, Green RD Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 2002, 12:1749-1755.
169. Katagiri F, Glazebrook J. Overview of mRNA expression profiling using microarrays. Curr Protoc Mol Biol 2004. Chapter 22: Unit 22 24.
170. Bolstad BM, Irizarry RA, Astrand M, Speed TP A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193.
171. Quackenbush J Microarray data normalization and transformation. Nat Genet 2002, 32(Suppl):496-501.
172. Page GP, Zakharkin SO, Kim K, Mehta T, Chen L, Zhang K Microarray analysis. Methods Mol Biol 2007, 404:409-430.
173. Simon R Challenges of microarray data and the evaluation of gene expression profile signatures. Cancer Invest 2008, 26:327-332.
174. Simon R Microarray-based expression profiling and informatics. Curr Opin Biotechnol 2008, 19:26-29.
175. Yang JY Microarrays-planning your experiment. Methods Mol Med 2008, 141:71-85.
176. Tusher VG, Tibshirani R, Chu G Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121.
177. Gautier L, Cope L, Bolstad BM, Irizarry RA Affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315.
178. Mutwil M, Obro J, Willats WG, Persson S GeneCAT-novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Res 2008, 36:W320-W326.
179. Comelli EM, Sutton-Smith M, Yan Q, Amado M, Panico M, Gilmartin T, Whisenant T, Lanigan CM, Head SR, Goldberg D, Morris HR, Dell A, Paulson JC Activation of murine CD4+ and CD8+ T lymphocytes leads to dramatic remodeling of N-linked glycans. J Immunol 2006, 177:2431-2440.
180. Tribulatti MV, Mucci J, Cattaneo V, Aguero F, Gilmartin T, Head SR, Campetella O Galectin-8 induces apoptosis in the CD4(high)CD8(high) thymocyte subpopulation. Glycobiology 2007, 17:1404-1412.
181. Kobayashi M, Lee H, Schaffer L, Gilmartin TJ, Head SR, Takaishi S, Wang TC, Nakayama J, Fukuda M A distinctive set of genes is upregulated during the inflammation-carcinoma sequence in mouse stomach infected by Helicobacter felis. J Histochem Cytochem 2007, 55:263-274.
182. Desplats PA, Denny CA, Kass KE, Gilmartin T, Head SR, Sutcliffe JG, Seyfried TN, Thomas EA Glycolipid and ganglioside metabolism imbalances in Huntington's disease. Neurobiol Dis 2007, 27:265-277.
183. Sampathkumar SG, Jones MB, Meledeo MA, Campbell CT, Choi SS, Hida K, Gomutputra P, Sheh A, Gilmartin T, Head SR, Yarema KJ Targeting glycosylation pathways and the cell cycle: sugar-dependent activity of butyrate-carbohydrate cancer prodrugs. Chem Biol 2006, 13:1265-1275.
184. Narayan S, Head SR, Gilmartin TJ, Dean B, Thomas EA Evidence for disruption of sphingolipid metabolism in schizophrenia. J Neurosci Res 2008, 87:278-288.
185. Marcos NT, Magalhaes A, Ferreira B, Oliveira MJ, Carvalho AS, Mendes N, Gilmartin T, Head SR, Figueiredo C, David L, Santos-Silva F, Reis CA Helicobacter pylori induces beta3GnT5 in human gastric cell lines, modulating expression of the SabA ligand sialyl-Lewis x. J Clin Invest 2008, 118:2325-2336.
186. Diskin S, Kumar J, Cao Z, Schuman JS, Gilmartin T, Head SR, Panjwani N Detection of differentially expressed glycogenes in trabecular meshwork of eyes with primary open-angle glaucoma. Invest Ophthalmol Vis Sci 2006, 47:1491-1499.
187. Kroes RA, Dawson G, Moskal JR Focused microarray analysis of glyco-gene expression in human glioblastomas. J Neurochem 2007, 103(Suppl 1):14-24.
188. Andre S, Sanchez-Ruderisch H, Nakagawa H, Buchholz M, Kopitz J, Forberich P, Kemmner W, Bock C, Deguchi K, Detjen KM, Wiedenmann B, von Knebel Doeberitz M, Gress TM, Nishimura S, Rosewicz S, Gabius HJ Tumor suppressor p16INK4a-modulator of glycomic profile and galectin-1 expression to increase susceptibility to carbohydrate-dependent induction of anoikis in pancreatic carcinoma cells. FEBS J 2007, 274:3233-3256.
189. Hood LE, Hunkapiller MW, Smith LM Automated DNA sequencing and analysis of the human genome. Genomics 1987, 1:201-212.
190. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 1991, 252:1651-1656.
191. Boguski MS, Lowe TM, Tolstoshev CM dbEST-database for "expressed sequence tags.". Nat Genet 1993, 4:332-333.
192. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW Serial analysis of gene expression. Science 1995, 270:484-487.
193. Polyak K, Riggins GJ Gene discovery using the serial analysis of gene expression technique: implications for cancer research. J Clin Oncol 2001, 19:2948-2958.
194. Yamamoto M, Wakatsuki T, Hada A, Ryo A Use of serial analysis of gene expression (SAGE) technology. J Immunol Methods 2001, 250:45-66.
195. Ryo A, Kondoh N, Wakatsuki T, Hada A, Yamamoto N, Yamamoto M A modified serial analysis of gene expression that generates longer sequence tags by nonpalindromic cohesive linker ligation. Anal Biochem 2000, 277:160-162.
196. Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, Carninci P, Hayashizaki Y Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci USA 2003, 100:15776-15781.
197. de Hoon M, Hayashizaki Y Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference. Biotechniques 2008, 44:627-632.
198. Silva WA, Covas DT, Panepucci RA, Proto-Siqueira R, Siufi JL, Zanette DL, Santos AR, Zago MA. The profile of gene expression of human marrow mesenchymal stem cells. Stem Cells 2003, 21:661-669.
199. Chu TJ, Peters DG Serial analysis of the vascular endothelial transcriptome under static and shear stress conditions. Physiol Genomics 2008, 34:185-192.
200. Shendure JA, Porreca GJ, Church GM. Overview of DNA sequencing strategies. Curr Protoc Mol Biol 2008. Chapter 7: Unit 7 1.
201. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
202. Ronaghi M, Uhlen M, Nyren P A sequencing method based on real-time pyrophosphate. Science 1998, 281:363-365.
203. Brenner S, Williams SR, Vermaas EH, Storck T, Moon K, McCollum C, Mao JI, Luo S, Kirchner JJ, Eletr S, DuBridge RB, Burcham T, Albrecht G In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci USA 2000, 97:1665-1670.
204. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 2000, 18:630-634.
205. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Res 2005, 33:D562-D566.
206. Mullis KB Target amplification for DNA analysis by the polymerase chain reaction. Ann Biol Clin (Paris) 1990, 48:579-582.
207. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 1985, 230:1350-1354.
208. Powell LM, Wallis SC, Pease RJ, Edwards YH, Knott TJ, Scott J A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 1987, 50:831-840.
209. Wong H, Muzik H, Groft LL, Lafleur MA, Matouk C, Forsyth PA, Schultz GA, Wall SJ, Edwards DR Monitoring MMP and TIMP mRNA expression by RT-PCR. Methods Mol Biol 2001, 151:305-320.
210. Wells GM, Catlin G, Cossins JA, Mangan M, Ward GA, Miller KM, Clements JM Quantitation of matrix metalloproteinases in cultured rat astrocytes using the polymerase chain reaction with a multi-competitor cDNA standard. Glia 1996, 18:332-340.
211. Vu HL, Troubetzkoy S, Nguyen HH, Russell MW, Mestecky J A method for quantification of absolute amounts of nucleic acids by (RT)-PCR and a new mathematical model for data analysis. Nucleic Acids Res 2000, 28:E18.
212. Cha RS, Thilly WG Specificity, efficiency, and fidelity of PCR. PCR Methods Appl 1993, 3:S18-S29.
213. Zhao S, Consoli U, Arceci R, Pfeifer J, Dalton WS, Andreeff M Semi-automated PCR method for quantitating MDR1 expression. Biotechniques 1996, 21:726-731.
214. Kobayashi M Expression profiling of glycosyltransferases using RT-PCR. Methods Enzymol 2006, 416:129-140.
215. Li X, Bratton S, Radominska-Pandya A Human UGT1A8 and UGT1A10 mRNA are expressed in primary human hepatocytes. Drug Metab Pharmacokinet 2007, 22:152-161.
216. Yamamoto M, Yamamoto F, Luong TT, Williams T, Kominato Y Expression profiling of 68 glycosyltransferase genes in 27 different human tissues by the systematic multiplex reverse transcription-polymerase chain reaction method revealed clustering of sexually related tissues in hierarchical clustering algorithm analysis. Electrophoresis 2003, 24:2295-2307.
217. Heid CA, Stevens J, Livak KJ, Williams PM Real time quantitative PCR. Genome Res 1996, 6:986-994.
218. Steuerwald N, Cohen J, Herrera RJ, Brenner CA Analysis of gene expression in single oocytes and embryos by real-time rapid cycle fluorescence monitored RT-PCR. Mol Hum Reprod 1999, 5:1034-1039.
219. Gibson UE, Heid CA, Williams PM A novel method for real time quantitative RT-PCR. Genome Res 1996, 6:995-1001.
220. Schmittgen TD, Zakrajsek BA, Mills AG, Gorn V, Singer MJ, Reed MW Quantitative reverse transcription-polymerase chain reaction to study mRNA decay: comparison of endpoint and real-time methods. Anal Biochem 2000, 285:194-204.
221. Bustin SA Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 2000, 25:169-193.
222. Pfaffl MW A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001, 29:e45.
223. Pfaffl MW, Hageleit M Validities of mRNA quantification using recombinant RNA and recombinant DNA external calibration curves in real-time RT-PCR. Biotechnol Lett 2001, 23:275-282.
224. Livak KJ, Schmittgen TD Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25:402-408.
225. Schmittgen TD, Lee EJ, Jiang J High-throughput real-time PCR. Methods Mol Biol 2008, 429:89-98.
226. Schmittgen TD, Livak KJ Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 2008, 3:1101-1108.
227. Morrison TB, Weis JJ, Wittwer CT Quantification of low-copy transcripts by continuous SYBR (R) green I monitoring during amplification. Biotechniques 1998, 24:954-958.
228. Karlsen F, Steen HB, Nesland JM SYBR green I DNA staining increases the detection sensitivity of viruses by polymerase chain reaction. J Virol Methods 1995, 55:153-156.
229. Mao F, Leung WY, Xin X Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnol 2007, 7:76.
230. Ahmad AI BOXTO as a real-time thermal cycling reporter dye. J Biosci 2007, 32:229-239.
231. Ponchel F Real-time PCR using SYBR Green. Real-time PCR 2006, 139-154. Taylor & Francis Group, New York. M.T. Dorak (Ed.).
232. Bernard PS, Ajioka RS, Kushner JP, Wittwer CT Homogeneous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes. Am J Pathol 1998, 153:1055-1061.
233. Tyagi S, Kramer FR Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 1996, 14:303-308.
234. Nazarenko I, Lowe B, Darfler M, Ikonomi P, Schuster D, Rashtchian A Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore. Nucleic Acids Res 2002, 30:e37.
235. Whitcombe D, Theaker J, Guy SP, Brown T, Little S Detection of PCR products using self-probing amplicons and fluorescence. Nat Biotechnol 1999, 17:804-807.
236. Bustin SA, editor. A-Z of Quantitative PCR. In: Tsigelny IF, editor. IUL Biotechnology Series. La Jolla: International University Line; 2004, p. 882.
237. Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y, Maqsodi B, Papallo A, Peters EH, Poulter K, Ruppel PL, Samaha RR, Shi L, Yang W, Zhang L, Goodsaid FM Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 2006, 24:1115-1122.
238. Provenzano M, Mocellin S Complementary techniques: validation of gene expression data by quantitative real time PCR. Adv Exp Med Biol 2007, 593:66-73.
239. Morrison T, Hurley J, Garcia J, Yoder K, Katz A, Roberts D, Cho J, Kanigan T, Ilyin SE, Horowitz D, Dixon JM, Brenan CJ Nanoliter high throughput quantitative PCR. Nucleic Acids Res 2006, 34:e123.
240. King KR, Wang S, Irimia D, Jayaraman A, Toner M, Yarmush ML A high-throughput microfluidic real-time gene expression living cell array. Lab Chip 2007, 7:77-85.
241. Guo JM, Chen HL, Wang GM, Zhang YK, Narimatsu H Expression of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-12 in gastric and colonic cancer cell lines and in human colorectal cancer. Oncology 2004, 67:271-276.
242. Tan S, Cheng PW Mucin biosynthesis: identification of the cis-regulatory elements of human C2GnT-M gene. Am J Respir Cell Mol Biol 2007, 36:737-745.
243. Hameetman L, David G, Yavas A, White SJ, Taminiau AH, Cleton-Jansen AM, Hogendoorn PC, Bovee JV Decreased EXT expression and intracellular accumulation of heparan sulphate proteoglycan in osteochondromas and peripheral chondrosarcomas. J Pathol 2007, 211:399-409.
244. Avril T, North SJ, Haslam SM, Willison HJ, Crocker PR Probing the cis interactions of the inhibitory receptor Siglec-7 with alpha2,8-disialylated ligands on natural killer cells and other leukocytes using glycan-specific antibodies and by analysis of alpha2,8-sialyltransferase gene expression. J Leukoc Biol 2006, 80:787-796.
245. Stamatos NM, Liang F, Nan X, Landry K, Cross AS, Wang LX, Pshezhetsky AV Differential expression of endogenous sialidases of human monocytes during cellular differentiation into macrophages. FEBS J 2005, 272:2545-2556.
246. Garcia-Vallejo JJ, van Dijk W, van Die I, Gringhuis SI Tumor necrosis factor-alpha up-regulates the expression of beta1,4-galactosyltransferase I in primary human endothelial cells by mRNA stabilization. J Biol Chem 2005, 280:12676-12682.
247. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4:P3.
248. Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA Global functional profiling of gene expression. Genomics 2003, 81:98-104.
249. Arakawa K, Kono N, Yamada Y, Mori H, Tomita M KEGG-based pathway visualization tool for complex omics data. In Silico Biol 2005, 5:419-423.
250. Wu J, Mao X, Cai T, Luo J, Wei L KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res 2006, 34:W720-W724.
251. Xia Y, Campen A, Rigsby D, Guo Y, Feng X, Su EW, Palakal M, Li S DGEM-a microarray gene expression database for primary human disease tissues. Mol Diagn Ther 2007, 11:145-149.
252. Cavalieri D, Castagnini C, Toti S, Maciag K, Kelder T, Gambineri L, Angioli S, Dolara P Eu. Gene Analyzer: a tool for integrating gene expression data with pathway databases. Bioinformatics 2007, 23:2631-2632.
253. Werner T Bioinformatics applications for pathway analysis of microarray data. Curr Opin Biotechnol 2008, 19:50-54.
254. Krambeck FJ, Betenbaugh MJ A mathematical model of N-linked glycosylation. Biotechnol Bioeng 2005, 92:711-728.