Comparative gene expression analysis of murine retina and brain

Molecular Vision

Volumn 10, Issue , 2004, Pages 637-649

  Hackam, Abigail S ^a,d   Qian, Jiang ^a   Liu, Dongmei ^b   Gunatilaka, Tushara ^a   Farkas, Ronald H ^a   Chowers, Itay ^a   Kageyama, Masaaki ^c   Parmigiani, Giovanni ^b   Zack, Donald J ^a,b  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c SANTEN PHARMACEUTICAL CO LTD   (Japan)

^d UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; POLYCYTIDYLIC ACID BINDING PROTEIN 1; REGULATOR PROTEIN; RNA; RNA BINDING PROTEIN; RNA BINDING PROTEIN EWS; UNCLASSIFIED DRUG; EYE PROTEIN; NERVE PROTEIN;

ANALYTIC METHOD; ANIMAL TISSUE; ARTICLE; BRAIN; CELLULAR DISTRIBUTION; CENTRAL NERVOUS SYSTEM; COMPARATIVE GENE MAPPING; COMPUTER PROGRAM; CONTROLLED STUDY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; HIGH THROUGHPUT SCREENING; IMAGE ANALYSIS; IMMUNOHISTOCHEMISTRY; INTERMETHOD COMPARISON; LIVER; MOUSE; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RETINA; RNA HYBRIDIZATION; SERIAL ANALYSIS OF GENE EXPRESSION; STATISTICAL ANALYSIS; TRANSCRIPTION REGULATION; ANIMAL; COMPARATIVE STUDY; GENE EXPRESSION; GENETICS; METABOLISM; NUCLEIC ACID HYBRIDIZATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANIMALS; BRAIN; EXPRESSED SEQUENCE TAGS; EYE PROTEINS; GENE EXPRESSION; GENE EXPRESSION PROFILING; IMMUNOHISTOCHEMISTRY; LIVER; MICE; NERVE TISSUE PROTEINS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RETINA; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA;

EID: 7044286092     PISSN: 10900535     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (42)

1. Swaroop A, Zack DJ. Transcriptome analysis of the retina. Genome Biol 2002; 3:REVIEWS1022.
2. Wilson AS, Hobbs BG, Speed TP, Rakoczy PE. The microarray: potential applications for ophthalmic research. Mol Vis 2002; 8:259-70 .
3. Farjo R, Yu J, Othman MI, Yoshida S, Sheth S, Glaser T, Baehr W, Swaroop A. Mouse eye gene microarrays for investigating ocular development and disease. Vision Res 2002; 42:463-70.
4. Hackam AS, Strom R, Liu D, Qian J, Wang C, Otteson D, Gunatilaka T, Farkas RH, Chowers I, Kageyama M, Leveillard T, Sahel JA, Campochiaro PA, Parmigiani G, Zack DJ. Identification of Gene Expression Changes Associated with the Progression of Retinal Degeneration in the rd1 Mouse. Invest Ophthalmol Vis Sci 2004; 45:2929-42.
5. Diaz E, Yang YH, Ferreira T, Loh KC, Okazaki Y, Hayashizaki Y, Tessier-Lavigne M, Speed TP, Ngai J. Analysis of gene expression in the developing mouse retina. Proc Natl Acad Sci U S A 2003; 100:5491-6.
6. Hackam AS, Bradford RL, Bakhru RN, Shah RM, Farkas R, Zack DJ, Adler R. Gene discovery in the embryonic chick retina. Mol Vis 2003; 9:262-76 .
7. Chowers I, Liu D, Farkas RH, Gunatilaka TL, Hackam AS, Bernstein SL, Campochiaro PA, Parmigiani G, Zack DJ. Gene expression variation in the adult human retina. Hum Mol Genet 2003; 12:2881-93.
8. Yoshida S, Yashar BM, Hiriyanna S, Swaroop A. Microarray analysis of gene expression in the aging human retina. Invest Ophthalmol Vis Sci 2002; 43:2554-60.
9. Chowers I, Gunatilaka TL, Farkas RH, Qian J, Hackam AS, Duh E, Kageyama M, Wang C, Vora A, Campochiaro PA, Zack DJ. Identification of novel genes preferentially expressed in the retina using a custom human retina cDNA microarray. Invest Ophthalmol Vis Sci 2003; 44:3732-41.
10. Blackshaw S, Fraioli RE, Furukawa T, Cepko CL. Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell 2001; 107:579-89.
11. Blackshaw S, Kuo WP, Park PJ, Tsujikawa M, Gunnersen JM, Scott HS, Boon WM, Tan SS, Cepko CL. MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol 2003; 4:R17.
12. Sharon D, Blackshaw S, Cepko CL, Dryja TP. Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE). Proc Natl Acad Sci U S A 2002; 99:315-20.
13. Yu J, Farjo R, MacNee SP, Baehr W, Stambolian DE, Swaroop A. Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina. Genome Biol 2003; 4:R65.
14. Mu X, Zhao S, Pershad R, Hsieh TF, Scarpa A, Wang SW, White RA, Beremand PD, Thomas TL, Gan L, Klein WH. Gene expression in the developing mouse retina by EST sequencing and microarray analysis. Nucleic Acids Res 2001; 29:4983-93.
15. Katsanis N, Worley KC, Gonzalez G, Ansley SJ, Lupski JR. A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. Proc Natl Acad Sci U S A 2002; 99:14326-31.
16. Bortoluzzi S, d'Alessi F, Danieli GA. A novel resource for the study of genes expressed in the adult human retina. Invest Ophthalmol Vis Sci 2000; 41:3305-8.
17. Sandberg R, Yasuda R, Pankratz DG, Carter TA, Del Rio JA, Wodicka L, Mayford M, Lockhart DJ, Barlow C. Regional and strain-specific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci U S A 2000; 97:11038-43.
18. Gunnersen JM, Augustine C, Spirkoska V, Kim M, Brown M, Tan SS. Global analysis of gene expression patterns in developing mouse neocortex using serial analysis of gene expression. Mol Cell Neurosci 2002; 19:560-73.
19. Gustincich S, Batalov S, Beisel KW, Bono H, Carninci P, Fletcher CF, Grimmond S, Hirokawa N, Jarvis ED, Jegla T, Kawasawa Y, LeMieux J, Miki H, Raviola E, Teasdale RD, Tominaga N, Yagi K, Zimmer A, Hayashizaki Y, Okazaki Y, RIKEN GER Group, GSL Members. Analysis of the mouse transcriptome for genes involved in the function of the nervous system. Genome Res 2003; 13:1395-401.
20. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-10.
21. 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; 31:219-23.
22. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-9.
23. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J. A concise guide to cDNA microarray analysis. Biotechniques 2000; 29:548-50,552-4,556.
24. Dudoit S, Yang JYH. Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In: Parmigiani G, Garrett ES, Irizarry RA, Zeger SL, editors. The analysis of gene expression data: methods and software. New York: Springer Verlag; 2003. p. 45-65.
25. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001; 98:5116-21. Erratum in: Proc Natl Acad Sci U S A 2001; 98:10515.
26. 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, Hogenesch JB. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 2002; 99:4465-70.
27. Simpson DA, Feeney S, Boyle C, Stitt AW. Retinal VEGF mRNA measured by SYBR green I fluorescence: A versatile approach to quantitative PCR. Mol Vis 2000; 6:178-83 .
28. Melot T, Dauphinot L, Sevenet N, Radvanyi F, Delattre O. Characterization of a new brain-specific isoform of the EWS oncoprotein. Eur J Biochem 2001; 268:3483-9.
29. Gamarnik AV, Andino R. Two functional complexes formed by KH domain containing proteins with the 5′ noncoding region of poliovirus RNA. RNA 1997; 3:882-92.
30. Ohno T, Rao VN, Reddy ES. EWS/Fli-1 chimeric protein is a transcriptional activator. Cancer Res 1993; 53:5859-63.
31. Ohno T, Ouchida M, Lee L, Gatalica Z, Rao VN, Reddy ES. The EWS gene, involved in Ewing family of tumors, malignant melanoma of soft parts and desmoplastic small round cell tumors, codes for an RNA binding protein with novel regulatory domains. Oncogene 1994; 9:3087-97.
32. Czyzyk-Krzeska MF, Bendixen AC. Identification of the poly(C) binding protein in the complex associated with the 3′ untranslated region of erythropoietin messenger RNA. Blood 1999; 93:2111-20.
33. Silvera D, Gamarnik AV, Andino R. The N-terminal K homology domain of the poly(rC)-binding protein is a major determinant for binding to the poliovirus 5′-untranslated region and acts as an inhibitor of viral translation. J Biol Chem 1999; 274:38163-70.
34. Waggoner SA, Liebhaber SA. Identification of mRNAs associated with alphaCP2-containing RNP complexes. Mol Cell Biol 2003; 23:7055-67.
35. Belyanskaya LL, Delattre O, Gehring H. Expression and subcellular localization of Ewing sarcoma (EWS) protein is affected by the methylation process. Exp Cell Res 2003; 288:374-81.
36. Bertolotti A, Melot T, Acker J, Vigneron M, Delattre O, Tora L. EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes. Mol Cell Biol 1998; 18:1489-97.
37. Araya N, Hirota K, Shimamoto Y, Miyagishi M, Yoshida E, Ishida J, Kaneko S, Kaneko M, Nakajima T, Fukamizu A. Cooperative interaction of EWS with CREB-binding protein selectively activates hepatocyte nuclear factor 4-mediated transcription. J Biol Chem 2003; 278:5427-32.
38. Felsch JS, Lane WS, Peralta EG. Tyrosine kinase Pyk2 mediates G-protein-coupled receptor regulation of the Ewing sarcoma RNA-binding protein EWS. Curr Biol 1999; 9:485-8.
39. Zhu Y, Sun Y, Mao XO, Jin KL, Greenberg DA. Expression of poly(C)-binding proteins is differentially regulated by hypoxia and ischemia in cortical neurons. Neuroscience 2002; 110:191-8.
40. Stohr H, Mah N, Schulz HL, Gehrig A, Frohlich S, Weber BH. EST mining of the UniGene dataset to identify retina-specific genes. Cytogenet Cell Genet 2000; 91:267-77.
41. Gottsch JD, Seitzman GD, Margulies EH, Bowers AL, Michels AJ, Saha S, Jun AS, Stark WJ, Liu SH. Gene expression in donor corneal endothelium. Arch Ophthalmol 2003; 121:252-8.
42. Evans SJ, Datson NA, Kabbaj M, Thompson RC, Vreugdenhil E, De Kloet ER, Watson SJ, Akil H. Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis. Serial Analysis of Gene Expression. Eur J Neurosci 2002; 16:409-13.