Synexpression analysis of ESTs in the rat brain reveals distinct patterns and potential drug targets

Brain research. Molecular brain research

Volumn 104, Issue 2, 2002, Pages 176-183

  Marvanova M ^a   Toronen P ^a   Storvik, M ^a   Lakso, M ^a   Castren E ^a   Wong, G ^a  

^a UNIVERSITY OF EASTERN FINLAND   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID RECEPTOR BLOCKING AGENT; COMPLEMENTARY DNA; MESSENGER RNA; NERVE PROTEIN; NEUROLEPTIC AGENT;

ANIMAL; ARTICLE; BIOSYNTHESIS; BRAIN; BRAIN MAPPING; CLUSTER ANALYSIS; CORPUS STRIATUM; CYTOLOGY; DRUG EFFECT; EXPRESSED SEQUENCE TAG; GENE LIBRARY; GENETICS; IN SITU HYBRIDIZATION; MALE; METABOLISM; NERVE CELL; PHYLOGENY; RAT; WISTAR RAT;

ANIMALS; ANTIPSYCHOTIC AGENTS; BRAIN; BRAIN MAPPING; CLUSTER ANALYSIS; CORPUS STRIATUM; DNA, COMPLEMENTARY; EXCITATORY AMINO ACID ANTAGONISTS; EXPRESSED SEQUENCE TAGS; GENOMIC LIBRARY; IN SITU HYBRIDIZATION; MALE; NERVE TISSUE PROTEINS; NEURONS; PHYLOGENY; RATS; RATS, WISTAR; RNA, MESSENGER;

EID: 0037103997     PISSN: 0169328X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-328X(02)00356-X     Document Type: Article

References (46)

1. M.D. Adams J.M. Kelley J.D. Gocayne M. Dubnick M.H. Polymeropoulos H. Xiao C.R. Merril A. Wu B. Olde R.F. Moreno Complementary DNA sequencing: expressed sequence tags and human genome project Science 252 1991 1651 1656
2. V.M. Brown A. Ossadtchi A.H. Khan S.R. Cherry R.M. Leahy D.J. Smith High-throughput imaging of brain gene expression Genome Res. 12 2002 244 254
3. M.F. Bonaldo G. Lennon M.B. Soares Normalization and subtraction: two approaches to facilitate gene discovery Genome Res. 6 1996 791 806
4. Y. Chen M.L. Bittner E.R. Rougherty Issues associated with microarray data analysis and integration Nat. Genet. 22 1999 213 215
5. R. Chen J.B. Bouck G.M. Weinstock R.A. Gibbs Comparing vertebrate whole-genome shotgun reads to the human genome Genome Res. 11 2001 1807 1816
6. E. Culetto D.B. Sattelle A role for Caenorhabditis elegans in understanding the function and interactions of human disease genes Hum. Mol. Genet. 9 2000 869 877
7. S.P. Damask K.A. Bovenkerk G. de la Pena K.M. Hoversten D.B. Peters A.M. Valentine J.H. Meador-Woodruff Differential effect of clozapine and haloperidol on dopamine receptor mRNA expression in rat striatum and cortex Brain Res. Mol. Brain Res. 41 1996 241 249
8. J.L. DeRisi V.R. Iyer P.O. Brown Exploring the metabolic and genetic control of gene expression on a genomic scale Science 278 1997 680 686
9. D.J. Duggan M. Bittner Y. Chen P. Meltzer J.M. Trent Expression profiling using cDNA microarrays Nat. Genet. 21 1999 10 14
10. B. Dysvik I. Jonassen J-Express: exploring gene expression data using JAVA Bioinformatics 17 2001 369 370
11. M.B. Eisen P.T. Spellman P.O. Brown D. Botstein Cluster analysis and display of genome-wide expression patterns Proc. Natl. Acad. Sci. USA 95 1998 14863 14868
12. S. Faranda A. Frattini I. Zucchi C. Patrosso L. Milanesi C. Montagna P. Vezzoni Characterization and fine localization of two new genes in Xq28 using the genomic sequence/EST database screening approach Genomics 34 1996 323 327
13. C.P. Fenster T.L. Whitworth E.B. Sheffield M.W. Quick R.A. Lester Upregulation of surface alpha4beta2 nicotinic receptors is initiated by receptor desensitization after chronic exposure to nicotine J. Neurosci. 19 1999 4804 4814
14. V. Gawantka N. Pollet H. Delius M. Vingron R. Pfister R. Nitsch C. Blumenstock C. Niehrs Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning Mech. Dev. 77 1998 95 141
15. P.E. Hardin L.M. Angerer S.H. Hardin R.C. Angerer W.H. Klein Spec2 genes of Strongylocentrotus purpuratus. Structure and differential expression in embryonic aboral ectoderm cells J. Mol. Biol. 5 1988 417 431
16. M.E. Harper L.M. Marselle In situ hybridization—application to gene localization and RNA detection Cancer Genet. Cytogenet. 19 1986 73 80
17. U. Herzig C. Cadenas F. Sieckmann W. Sierralta C. Thaller A. Visel G. Eichele Development of high-throughput tools to unravel the complexity of gene expression patterns in the mammalian brain Novartis Found. Symp. 239 2001 129 146
18. L.J. Heyer S. Kruglyak S. Yooseph Exploring expression data: identification and analysis of coexpressed genes Genome Res. 9 1999 1106 1115
19. R.L. Klein R.A. Harris Regulation of GABAA receptor structure and function by chronic drug treatments in vivo and with stably transfected cells Jpn. J. Pharmacol. 70 1996 1 15
20. A.M. Lindén J. Vaisanen M. Storvik M. Lakso E.R. Korpi G. Wong E. Castrén Uncompetitive antagonists of the N-methyl- d -aspartate (NMDA) receptors alter the mRNA expression of proteins associated with the NMDA receptor complex Pharmacol. Toxicol. 88 2000 98 105
21. A.M. Lindén M. Storvik M. Lakso A. Haapasalo D. Lee J.M. Witkin Y. Sei E. Castrén G. Wong Increased expression of neuronal Src and tyrosine phosphorylation of NMDA receptors in rat brain after systemic treatment with MK-801 Neuropharmacology 40 2001 469 481
22. M.A. Marra L. Hillier R.H. Waterston Expressed sequence tags—ESTablishing bridges between genomes Trends Genet. 14 1998 4 7
23. R. Matoba K. Kato C. Kurooka C. Maruyama Y. Sakakibara K. Matsubara Correlation between gene functions and developmental expression patterns in the mouse cerebellum Eur. J. Neurosci. 12 2000 1357 1371
24. A.M. McNicol M.A. Farquharson In situ hybridization and its diagnostic applications in pathology J. Pathol. 182 1997 250 261
25. M.C. Mhatre M.K. Ticku Chronic ethanol administration alters gamma-aminobutyric acidA receptor gene expression Mol. Pharmacol. 42 1992 415 422
26. R.J. Milner J.G. Sutcliffe Gene expression in rat brain Nucleic Acids Res. 11 1983 5497 5520
27. M. Mody Y. Cao Z. Cui K.Y. Tay A. Shyong E. Shimizu K. Pham P. Schultz D. Welsh J.Z. Tsien Genome-wide gene expression profiles of the developing mouse hippocampus Proc. Natl. Acad. Sci. USA 98 2001 8862 8867
28. W.J. Murphy, R. Stanyon, S.J. O’Brien, Evolution of mammalian genome organization inferred from comparative gene mapping, Genome Biol. 2 (2001) Reviews 5.1–5.8.
29. C. Niehrs N. Pollet Synexpression groups in eukaryotes Nature 402 1999 483 487
30. S.J. O’Brien, M. Menotti-Raymond, W.J. Murphy, W.G. Nash, J. Wienberg, R. Stanyon, N.G. Copeland, N.A. Jenkins, J.E. Womack, J.A. Marshall Graves, The promise of comparative genomics in mammals, Science 286 (1999) 458–462, 479–481.
31. G. Paxinos C. Watson The Rat Brain in Stereotaxic Coordinates 1986 Academic Press Sydney
32. G. Paxinos I. Törk L. Tecott K.L. Valentino Atlas of the Developing Rat Brain 1991 Academic Press San Diego, CA
33. A.E. Pollack Anatomy, physiology, and pharmacology of the basal ganglia Neurol. Clin. 19 2001 523 534
34. H.A. Ring J. Serra-Mestres Neuropsychiatry of the basal ganglia J. Neurol. Neurosurg. Psychiatry 72 2002 12 21
35. H. Roest Crollius O. Jaillon A. Bernot C. Dasilva L. Bouneau C. Fischer C. Fizames P. Wincker P. Brottier F. Quetier W. Saurin J. Weissenbach Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence Nat. Genet. 25 2000 235 238
36. R. Sandberg R. Yasuda D.G. Pankratz T.A. Carter J.A. Del Rio L. Wodicka M. Mayford D.J. Lockhart C. Barlow Regional and strain-specific gene expression mapping in the adult mouse brain Proc. Natl. Acad. Sci. USA 97 2000 11038 11043
37. M. Schena D. Shalon R.W. Davis P.O. Brown Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270 1995 467 470
38. R.R. Sokal C.D. Michener A statistical method for evaluating systematic relationships Univ. Kans. Sci. Bull. 38 1958 1409 1438
39. M. Storvik A.M. Lindén O. Kontkanen M. Lakso E. Castrén G. Wong Induction of cAMP response element modulator (CREM) and inducible cAMP early repressor (ICER) expression in rat brain by uncompetitive N-methyl- d -aspartate receptor antagonists J. Pharmacol. Exp. Ther. 294 2000 52 60
40. J.G. Sutcliffe P.E. Foye M.G. Erlander B.S. Hilbush L.J. Bodzin J.T. Durham K.W. Hasel TOGA: an automated parsing technology for analyzing expression of nearly all genes Proc. Natl. Acad. Sci. USA 97 2000 1976 1981
41. R.L. Tatusov E.V. Koonin D.J. Lipman A genomic perspective on protein families Science 278 1997 631 637
42. R.L. Tatusov D.A. Natale I.V. Garkavtsev T.A. Tatusova U.T. Shankavaram B.S. Rao B. Kiryutin M.Y. Galperin N.D. Fedorova E.V. Koonin The COG database: new developments in phylogenetic classification of proteins from complete genomes Nucleic Acids Res. 29 2001 22 28
43. V.E. Velculescu L. Zhang B. Vogelstein K.W. Kinzler Serial analysis of gene expression Science 270 1995 484 487
44. W.W. Wasserman M. Palumbo W. Thompson J.W. Fickett C.E. Lawrence Human–mouse genome comparisons to locate regulatory sites Nat. Genet. 26 2000 225 228
45. X. Wen S. Fuhrman G.S. Michaels D.B. Carr S. Smith J.L. Barker R. Somogyi Large-scale temporal gene expression mapping of central nervous system development Proc. Natl. Acad. Sci. USA 95 1998 334 339
46. W. Wisden B. Morris In situ hybridization with synthetic oligonucleotide probes W. Wisden B. Morris In Situ Hybridization Protocols for Neurobiology 1994 Academic Press London 1 34