Congruence of tissue expression profiles from gene expression Atlas, SAGEmap and TissueInfo databases

BMC Genomics

Volumn 4, Issue , 2003, Pages

  Huminiecki, Lukasz ^a   Lloyd, Andrew T ^a   Wolfe, Kenneth H ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

ACCURACY; BRAIN TISSUE; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA BASE; EXPERIMENTATION; EXPRESSED SEQUENCE TAG; FACTUAL DATABASE; GENE EXPRESSION; GENE EXPRESSION ATLAS; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE OVEREXPRESSION; INFORMATION PROCESSING; KIDNEY; OVARY; PANCREAS; PREDICTION; PROSTATE; REVIEW; SAGEMAP; SAMPLE; SERIAL ANALYSIS OF GENE EXPRESSION; TISSUE SPECIFICITY; TISSUEINFO; VASCULAR ENDOTHELIUM; ARTICLE; BIOLOGY; BRAIN; COMPARATIVE STUDY; DNA MICROARRAY; FEMALE; GENETIC DATABASE; HUMAN; MALE; METABOLISM; METHODOLOGY; STANDARD; STATISTICS;

BRAIN; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; ENDOTHELIUM, VASCULAR; EXPRESSED SEQUENCE TAGS; FEMALE; GENE EXPRESSION PROFILING; HUMANS; KIDNEY; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OVARY; PANCREAS; PROSTATE; STATISTICS AS TOPIC;

EID: 9144244440     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-4-31     Document Type: Review

References (86)

1. Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ and Altschul SF: SAGEmap: a public gene expression resource Genome Res 2000, 10:1051-1060.
2. Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D and Brown PO: Systematic variation in gene expression patterns in human cancer cell lines Nat Genet 2000, 24:227-235.
3. Bortoluzzi S, d'Alessi F, Romualdi C and Danieli GA: The human adult skeletal muscle transcriptional profile reconstructed by a novel computational approach Genome Res 2000, 10:344-349.
4. Vasmatzis G, Essand M, Brinkmann U, Lee B and Pastan I: Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis Proc Natl Acad Sci U S A 1998, 95:300-304.
5. Itoh K, Okubo K, Utiyama H, Hirano T, Yoshii J and Matsubara K: Expression profile of active genes in granulocytes Blood 1998, 92:1432-1441.
6. Moreno JC, Pauws E, van Kampen AH, Jedlickova M, de Vijlder JJ and Ris-Stalpers C: Cloning of tissue-specific genes using serial analysis of gene expression and a novel computational substraction approach Genomics 2001, 75:70-76.
7. St Croix B, Rago C, Velculescu V, Traverso G, Romans KE, Montgomery E, Lal A, Riggins GJ, Lengauer C, Vogelstein B and Kinzler KW: Genes expressed in human tumor endothelium Science 2000, 289:1197-1202.
8. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, Heisterkamp S, van Kampen A and Versteeg R: The human transcriptome map: clustering of highly expressed genes in chromosomal domains Science 2001, 291:1289-1292.
9. Lercher MJ, Urrutia AO and Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in the human genome Nat Genet 2002, 31:180-183.
10. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L and Kohane IS: Analysis of matched mRNA measurements from two different microarray technologies Bioinformatics 2002, 18:405-412.
11. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG and Hogenesch JB: Large-scale analysis of the human and mouse transcriptomes Proc Natl Acad Sci U S A 2002, 99: 465-4470.
12. Skrabanek L and Campagne F: TissueInfo: high-throughput identification of tissue expression profiles and specificity Nucleic Acids Res 2001, 29:E102-2.
13. Huminiecki L and Bicknell R: In silico cloning of novel endothelial-specific genes Genome Res 2000, 10:1796-1806.
14. Farnsworth WE: Prostate stroma: physiology Prostate 1999, 38:60-72.
15. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H and Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays Nat Biotechnol 1996, 14:1675-1680.
16. Man MZ, Wang X and Wang Y: POWER_SAGE: comparing statistical tests for SAGE experiments Bioinformatics 2000, 16:953-959.
17. Romualdi C, Bortoluzzi S and Danieli GA: Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests Hum Mol Genet 2001, 10:2133-2141.
18. Chen C, Rainnie DG, Greene RW and Tonegawa S: Abnormal fear response and aggressive behavior in mutant mice deficient for alpha-calcium-calmodulin kinase II Science 1994, 266: 91-294.
19. Martin-Vasallo P, Dackowski W, Emanuel JR and Levenson R: Identification of a putative isoform of the Na,K-ATPase beta subunit. Primary structure and tissue-specific expression J Biol Chem 1989, 264:4613-4618.
20. Pagliusi S, Antonicek H, Gloor S, Frank R, Moos M and Schachner M: Identification of a cDNA clone specific for the neural cell adhesion molecule AMOG J Neurosci Res 1989, 22: 13-119.
21. Lien LL, Feener CA, Fischbach N and Kunkel LM: Cloning of human microtubule-associated protein 1B and the identification of a related gene on chromosome 15 Genomics 1994, 22:273-280.
22. Hu K, Carroll J, Fedorovich S, Rickman C, Sukhodub A and Davletov B: Vesicular restriction of synaptobrevin suggests a role for calcium in membrane fusion Nature 2002, 415:646-650.
23. Polymeropoulos MH, Ide S, Soares MB and Lennon GG: Sequence characterization and genetic mapping of the human VSNL1 gene, a homologue of the rat visinin-like peptide RNVP1 Genomics 1995, 29:273-275.
24. Diehl HJ, Schaich M, Budzinski RM and Stoffel W: Individual exons encode the integral membrane domains of human myelin proteolipid protein Proc Natl Acad Sci U S A 1986, 83: 807-9811.
25. Jiang M, Gold MS, Boulay G, Spicher K, Peyton M, Brabet P, Srinivasan Y, Rudolph U, Ellison G and Birnbaumer L: Multiple neurological abnormalities in mice deficient in the G protein Go Proc Natl Acad Sci U S A 1998, 95:3269-3274.
26. Strathmann M, Wilkie TM and Simon MI: Alternative splicing produces transcripts encoding two forms of the alpha subunit of GTP-binding protein Go Proc Natl Acad Sci U S A 1990, 87: 477-6481.
27. Yan Y, Lagenaur C and Narayanan V: Molecular cloning of M6: identification of a PLP/DM20 gene family Neuron 1993, 11: 23-431.
28. Eylar EH, Brostoff S, Hashim G, Caccam J and Burnett P: Basic A1 protein of the myelin membrane. The complete amino acid sequence J Biol Chem 1971, 246:5770-5784.
29. Wasco W, Bupp K, Magendantz M, Gusella JF, Tanzi RE and Solomon F: Identification of a mouse brain cDNA that encodes a protein related to the Alzheimer disease-associated amyloid beta protein precursor Proc Natl Acad Sci U S A 1992, 89:10758-10762.
30. Kedra D, Pan HQ, Seroussi E, Fransson I, Guilbaud C, Collins JE, Dunham I, Blennow E, Roe BA, Piehl F and Dumanski JP: Characterization of the human synaptogyrin gene family Hum Genet 1998, 103:131-141.
31. Fernandez-Chacon R, Konigstorfer A, Gerber SH, Garcia J, Matos MF, Stevens CF, Brose N, Rizo J, Rosenmund C and Sudhof TC: Synaptotagmin I functions as a calcium regulator of release probability Nature 2001, 410:41-49.
32. Nakagawa H, Koyama K, Murata Y, Morito M, Akiyama T and Nakamura Y: APCL, a central nervous system-specific homologue of adenomatous polyposis coli tumor suppressor, binds to p53-binding protein 2 and translocates it to the perinucleus Cancer Res 2000, 60: 01-105.
33. Strittmatter SM, Fankhauser C, Huang PL, Mashimo H and Fishman MC: Neuronal pathfinding is abnormal in mice lacking the neuronal growth cone protein GAP-43 Cell 1995, 80:445-452.
34. Bellingham J, Gregory-Evans K and Gregory-Evans CY: Sequence and tissue expression of a novel human carbonic anhydraserelated protein, CARP-2, mapping to chromosome 19q13.3 Biochem Biophys Res Commun 1998, 253:364-367.
35. Pevsner J, Hsu SC and Scheller RH: n-Sec1: a neural-specific syntaxin-binding protein Proc Natl Acad Sci U S A 1994, 91:1445-1449.
36. Schweitzer B, Taylor V, Welcher AA, McClelland M and Suter U: Neural membrane protein 35 (NMP35): a novel member of a gene family which is highly expressed in the adult nervous system Mol Cell Neurosci 1998, 11:260-273.
37. Bajjalieh SM, Peterson K, Linial M and Scheller RH: Brain contains two forms of synaptic vesicle protein 2 Proc Natl Acad Sci U S A 1993, 90:2150-2154.
38. Zhou RH, Kokame K, Tsukamoto Y, Yutani C, Kato H and Miyata T: Characterization of the human NDRG gene family: a newly identified member, NDRG4, is specifically expressed in brain and heart Genomics 2001, 73:86-97.
39. Craxton M: Genomic analysis of synaptotagmin genes Genomics 2001, 77:43-49.
40. Li SH, McInnis MG, Margolis RL, Antonarakis SE and Ross CA: Novel triplet repeat containing genes in human brain: cloning, expression, and length polymorphisms Genomics 1993, 16: 72-579.
41. Zemni R, Bienvenu T, Vinet MC, Sefiani A, Carrie A, Billuart P, McDonell N, Couvert P, Francis F, Chafey P, Fauchereau F, Friocourt G, Portes V, Cardona A, Frints S, Meindl A, Brandau O, Ronce N, Moraine C, Bokhoven H, Ropers HH, Sudbrak R, Kahn A, Fryns JP, Beldjord C and Chelly J: A new gene involved in X-linked mental retardation identified by analysis of an X;2 balanced translocation Nat Genet 2000, 24: 67-170.
42. Rall S. C., Jr., Weisgraber KH and Mahley RW: Human apolipoprotein E. The complete amino acid sequence J Biol Chem 1982, 257:4171-4178.
43. van der Bliek AM, Redelmeier TE, Damke H, Tisdale EJ, Meyerowitz EM and Schmid SL: Mutations in human dynamin block an intermediate stage in coated vesicle formation J Cell Biol 1993, 122:553-563.
44. Reddy TR, Li X, Jones Y, Ellisman MH, Ching GY, Liem RK and Wong-Staal F: Specific interaction of HTLV tax protein and a human type IV neuronal intermediate filament protein Proc Natl Acad Sci U S A 1998, 95:702-707.
45. Oliva D, Cali L, Feo S and Giallongo A: Complete structure of the human gene encoding neuron-specific enolase Genomics 1991, 10:157-165.
46. Stein R, Mori N, Matthews K, Lo LC and Anderson DJ: The NGFinducible SCG10 mRNA encodes a novel membrane-bound protein present in growth cones and abundant in developing neurons Neuron 1988, 1:463-476.
47. Ju YT, Chang AC, She BR, Tsaur ML, Hwang HM, Chao CC, Cohen SN and Lin-Chao S: gas7: A gene expressed preferentially in growth-arrested fibroblasts and terminally differentiated Purkinje neurons affects neurite formation Proc Natl Acad Sci U S A 1998, 95:11423-11428.
48. Zieger B, Tran H, Hainmann I, Wunderle D, Zgaga-Griesz A, Blaser S and Ware J: Characterization and expression analysis of two human septin genes, PNUTL1 and PNUTL2 Gene 2000, 261: 97-203.
49. Tanaka M, Tanaka T, Kijima H, Itoh J, Matsuda T, Hori S and Yamamoto M: Characterization of tissue- and cell-type-specific expression of a novel human septin family gene, Bradeion Biochem Biophys Res Commun 2001, 286:547-553.
50. Dou D and Joseph R: Cloning of human neuronatin gene and its localization to chromosome-20q 11.2-12: the deduced protein is a novel "proteolipid' Brain Res 1996, 723:8-22.
51. Kukita A, Mukai T, Miyata T and Hori K: The structure of brainspecific rat aldolase C mRNA and the evolution of aldolase isozyme genes Eur J Biochem 1988, 171:471-478.
52. Perez F, Pernet-Gallay K, Nizak C, Goodson HV, Kreis TE and Goud B: CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging to the CLIP-170 family J Cell Biol 2002, 156: 31-642.
53. Vannahme C, Schubel S, Herud M, Gosling S, Hulsmann H, Paulsson M, Hartmann U and Maurer P: Molecular cloning of testican-2: defining a novel calcium-binding proteoglycan family expressed in brain J Neurochem 1999, 73:12-20.
54. Frank M: MAL, a proteolipid in glycosphingolipid enriched domains: functional implications in myelin and beyond Prog Neurobiol 2000, 60:531-544.
55. Janoueix-Lerosey I, Pasheva E, de Tand MF, Tavitian A and de Gunzburg J: Identification of a specific effector of the small GTPbinding protein Rap2 Eur J Biochem 1998, 0252:290-298.
56. Li Y, Chin LS, Weigel C and Li L: Spring, a novel RING finger protein that regulates synaptic vesicle exocytosis J Biol Chem 2001, 276:40824-40833.
57. Wang W, Zhou Z, Zhao W, Huang Y, Tang R, Ying K, Xie Y and Mao Y: Molecular cloning, mapping and characterization of the human neurocalcin delta gene (NCALD) Biochim Biophys Acta 2001, 1518:162-167.
58. Vives V, Alonso G, Solal AC, Joubert D and Legraverend C: Visualization of S100B-positive neurons and glia in the central nervous system of EGFP transgenic mice J Comp Neurol 2003, 457: 04-419.
59. Hernandez MC, Andres-Barquin PJ, Holt I and Israel MA: Cloning of human ENC-1 and evaluation of its expression and regulation in nervous system tumors Exp Cell Res 1998, 242:470-477.
60. Dalmau J, Gultekin SH, Voltz R, Hoard R, DesChamps T, Balmaceda C, Batchelor T, Gerstner E, Eichen J, Frennier J, Posner JB and Rosenfeld MR: Ma1, a novel neuron- and testis-specific protein, is recognized by the serum of patients with paraneoplastic neurological disorders Brain 1999, 122 ( Pt 1):27-39.
61. Sasaki K, Kurata-Miura K, Ujita M, Angata K, Nakagawa S, Sekine S, Nishi T and Fukuda M: Expression cloning of cDNA encoding a human beta-1,3-N-acetylglucosaminyltransferase that is essential for poly-N-acetyllactosamine synthesis Proc Natl Acad Sci U S A 1997, 94:14294-14299.
62. Morris R: Thy-1 in developing nervous tissue Dev Neurosci 1985, 7:133-160.
63. Hunt JM, Bommert K, Charlton MP, Kistner A, Habermann E, Augustine GJ and Betz H: A post-docking role for synaptobrevin in synaptic vesicle fusion Neuron 1994, 12:1269-1279.
64. Gumienny TL, Brugnera E, Tosello-Trampont AC, Kinchen JM, Haney LB, Nishiwaki K, Walk SF, Nemergut ME, Macara IG, Francis R, Schedl T, Qin Y, Van Aelst L, Hengartner MO and Ravichandran KS: CED-12/ELMO, a novel member of the CrkII/Dock180/Rac pathway, is required for phagocytosis and cell migration Cell 2001, 107:27-41.
65. Bressler SL, Gray MD, Sopher BL, Hu Q, Hearn MG, Pham DG, Dinulos MB, Fukuchi K, Sisodia SS, Miller MA, Disteche CM and Martin GM: cDNA cloning and chromosome mapping of the human Fe65 gene: interaction of the conserved cytoplasmic domains of the human beta-amyloid precursor protein and its homologues with the mouse Fe65 protein Hum Mol Genet 1996, 5:1589-1598.
66. Leung T, How BE, Manser E and Lim L: Cerebellar beta 2-chimaerin, a GTPase-activating protein for p21 ras-related rac is specifically expressed in granule cells and has a unique N-terminal SH2 domain J Biol Chem 1994, 269:12888-12892.
67. Jobsis GJ, Keizers H, Vreijling JP, de Visser M, Speer MC, Wolterman RA, Baas F and Bolhuis PA: Type VI collagen mutations in Bethlem myopathy, an autosomal dominant myopathy with contractures Nat Genet 1996, 14:113-115.
68. Grover J, Chen XN, Korenberg JR and Roughley PJ: The human lumican gene. Organization, chromosomal location, and expression in articular cartilage J Biol Chem 1995, 270:21942-21949.
69. Todd SC, Doctor VS and Levy S: Sequences and expression of six new members of the tetraspanin/TM4SF family Biochim Biophys Acta 1998, 1399:101-104.
70. Spurr NK, Durbin H, Sheer D, Parkar M, Bobrow L and Bodmer WF: Characterization and chromosomal assignment of a human cell surface antigen defined by the monoclonal antibody AUAI Int J Cancer 1986, 38:631-636.
71. Lai EC, Kao FT, Law ML and Woo SL: Assignment of the alpha 1-antitrypsin gene and a sequence-related gene to human chromosome 14 by molecular hybridization Am J Hum Genet 1983, 35:385-392.
72. Katahira J, Sugiyama H, Inoue N, Horiguchi Y, Matsuda M and Sugimoto N: Clostridium perfringens enterotoxin utilizes two structurally related membrane proteins as functional receptors in vivo J Biol Chem 1997, 272:26652-26658.
73. Nagase T, Miyajima N, Tanaka A, Sazuka T, Seki N, Sato S, Tabata S, Ishikawa K, Kawarabayasi Y and Kotani H: Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1 (supplement) DNA Res 1995, 2: 1-59.
74. Trask DK, Band V, Zajchowski DA, Yaswen P, Suh T and Sager R: Keratins as markers that distinguish normal and tumorderived mammary epithelial cells Proc Natl Acad Sci U S A 1990, 87: 319-2323.
75. Kulesh DA and Oshima RG: Complete structure of the gene for human keratin 18 Genomics 1989, 4:339-347.
76. Bader BL, Magin TM, Hatzfeld M and Franke WW: Amino acid sequence and gene organization of cytokeratin no. 19, an exceptional tail-less intermediate filament protein Embo J 1986, 5: 865-1875.
77. Mbikay M, Nolet S, Fournier S, Benjannet S, Chapdelaine P, Paradis G, Dube JY, Tremblay R, Lazure C and Seidah NG: Molecular cloning and sequence of the cDNA for a 94-amino-acid seminal plasma protein secreted by the human prostate DNA 1987, 6:23-29.
78. Sharief FS, Lee H, Leuderman MM, Lundwall A, Deaven LL, Lee CL and Li SS: Human prostatic acid phosphatase: cDNA cloning, gene mapping and protein sequence homology with lysosomal acid phosphatase Biochem Biophys Res Commun 1989, 160:79-86.
79. Lundwall A and Lilja H: Molecular cloning of human prostate specific antigen cDNA FEBS Lett 1987, 214: 17-322.
80. Matsuoka R, Yoshida MC, Furutani Y, Imamura S, Kanda N, Yanagisawa M, Masaki T and Takao A: Human smooth muscle myosin heavy chain gene mapped to chromosomal region 16q12 Am J Med Genet 1993, 46:61-67.
81. Laing NG, Wilton SD, Akkari PA, Dorosz S, Boundy K, Kneebone C, Blumbergs P, White S, Watkins H and Love DR: A mutation in the alpha tropomyosin gene TPM3 associated with autosomal dominant nemaline myopathy Nat Genet 1995, 9:75-79.
82. Maestrini E, Patrosso C, Mancini M, Rivella S, Rocchi M, Repetto M, Villa A, Frattini A, Zoppe M and Vezzoni P: Mapping of two genes encoding isoforms of the actin binding protein ABP-280, a dystrophin like protein, to Xq28 and to chromosome 7 Hum Mol Genet 1993, 2:761-766.
83. Solway J, Seltzer J, Samaha FF, Kim S, Alger LE, Niu Q, Morrisey EE, Ip HS and Parmacek MS: Structure and expression of a smooth muscle cell-specific gene, SM22 alpha J Biol Chem 1995, 270:13460-13469.
84. Maric SC, Crozat A and Janne OA: Structure and organization of the human S-adenosylmethionine decarboxylase gene J Biol Chem 1992, 267:18915-18923.
85. Kumar CC and Chang C: Human smooth muscle myosin light chain-2 gene expression is repressed in ras transformed fibroblast cells Cell Growth Differ 1992, 3:1-10.
86. Lin B, White JT, Ferguson C, Wang S, Vessella R, Bumgarner R, True LD, Hood L and Nelson PS: Prostate short-chain dehydrogenase reductase 1 (PSDR1): a new member of the short-chain steroid dehydrogenase/reductase family highly expressed in normal and neoplastic prostate epithelium Cancer Res 2001, 61:1611-1618.