The retinome - Defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium

被引:26
作者
Schulz, HL
Goetz, T
Kaschkoetoe, J
Weber, BHF [1 ]
机构
[1] Univ Wurzburg, Bioctr, Inst Human Genet, D-97074 Wurzburg, Germany
[2] German Canc Res Ctr, Cent Spectroscop Dept, D-69120 Heidelberg, Germany
关键词
D O I
10.1186/1471-2164-5-50
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: The mammalian retina is a valuable model system to study neuronal biology in health and disease. To obtain insight into intrinsic processes of the retina, great efforts are directed towards the identification and characterization of transcripts with functional relevance to this tissue. Results: With the goal to assemble a first genome-wide reference transcriptome of the adult mammalian retina, referred to as the retinome, we have extracted 13,037 non-redundant annotated genes from nearly 500,000 published datasets on redundant retina/retinal pigment epithelium (RPE) transcripts. The data were generated from 27 independent studies employing a wide range of molecular and biocomputational approaches. Comparison to known retina-/RPE-specific pathways and established retinal gene networks suggest that the reference retinome may represent up to 90% of the retinal transcripts. We show that the distribution of retinal genes along the chromosomes is not random but exhibits a higher order organization closely following the previously observed clustering of genes with increased expression. Conclusion: The genome wide retinome map offers a rational basis for selecting suggestive candidate genes for hereditary as well as complex retinal diseases facilitating elaborate studies into normal and pathological pathways. To make this unique resource freely available we have built a database providing a query interface to the reference retinome [ 1].
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页数:11
相关论文
共 58 条
[1]   Chromosomal distribution of the human cardiovascular transcriptome [J].
Barrans, JD ;
Ip, J ;
Lam, CW ;
Hwang, IL ;
Dzau, VJ ;
Liew, CC .
GENOMICS, 2003, 81 (05) :519-524
[2]   Characterization of a human fovea cDNA library and regional differential gene expression in the human retina [J].
Bernstein, SL ;
Borst, DE ;
Neuder, ME ;
Wong, P .
GENOMICS, 1996, 32 (03) :301-308
[3]   MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues [J].
Blackshaw, S ;
Kuo, WP ;
Park, PJ ;
Tsujikawa, M ;
Gunnersen, JM ;
Scott, HS ;
Boon, WM ;
Tan, SS ;
Cepko, CL .
GENOME BIOLOGY, 2003, 4 (03)
[4]   Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes [J].
Blackshaw, S ;
Fraioli, RE ;
Furukawa, T ;
Cepko, CL .
CELL, 2001, 107 (05) :579-589
[5]  
Bortoluzzi S, 2000, INVEST OPHTH VIS SCI, V41, P3305
[6]   Alternative splicing and evolution [J].
Boue, S ;
Letunic, I ;
Bork, P .
BIOESSAYS, 2003, 25 (11) :1031-1034
[7]   The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags [J].
Brentani, H ;
Caballero, OL ;
Camargo, AA ;
da Silva, AM ;
da Silva, WA ;
Neto, ED ;
Grivet, M ;
Gruber, A ;
Guimaraes, PEM ;
Hide, W ;
Iseli, C ;
Jongeneel, CV ;
Kelso, J ;
Nagai, MA ;
Ojopi, EPB ;
Osorio, EC ;
Reis, EMR ;
Riggins, GJ ;
Simpson, AJG ;
de Souza, S ;
Stevenson, BJ ;
Strausberg, RL ;
Tajara, EH ;
Verjovski-Almeida, S ;
Acencion, ML ;
Bengtsono, MH ;
Bettonip, F ;
Bodmerq, WF ;
Brionesr, MRS ;
Camargos, LP ;
Caveneet, W ;
Ceruttiu, JM ;
Coelho Andradev, LE ;
Costa dos Santosn, PC ;
Costaw, MCR ;
da Silvaw, IT ;
Esteciox, MRH ;
Ferreiraw, KS ;
Furnarit, FB ;
Faria, M ;
Galantep, PAF ;
Guimaraesy, GS ;
Holandaw, AJ ;
Kimuraz, ET ;
Leerkesp, MR ;
Xin, LA ;
Macielu, RMB ;
Martinsbb, EAL ;
Massirero, KB ;
Melor, ASA .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (23) :13418-13423
[8]  
Buraczynska M, 2002, INVEST OPHTH VIS SCI, V43, P603
[9]   Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia [J].
Carninci, P ;
Waki, K ;
Shiraki, T ;
Konno, H ;
Shibata, K ;
Itoh, M ;
Aizawa, K ;
Arakawa, T ;
Ishii, Y ;
Sasaki, D ;
Bono, H ;
Kondo, S ;
Sugahara, Y ;
Saito, R ;
Osato, N ;
Fukuda, S ;
Sato, K ;
Watahiki, A ;
Hirozane-Kishikawa, T ;
Nakamura, M ;
Shibata, Y ;
Yasunishi, A ;
Kikuchi, N ;
Yoshiki, A ;
Kusakabe, M ;
Gustincich, S ;
Beisel, K ;
Pavan, W ;
Aidinis, V ;
Nakagawara, A ;
Held, WA ;
Iwata, H ;
Kono, T ;
Nakauchi, H ;
Lyons, P ;
Wells, C ;
Hume, DA ;
Fagiolini, M ;
Hensch, TK ;
Brinkmeier, M ;
Camper, S ;
Hirota, J ;
Mombaerts, P ;
Muramatsu, M ;
Okazaki, Y ;
Kawai, J ;
Hayashizaki, Y .
GENOME RESEARCH, 2003, 13 (6B) :1273-1289
[10]   The human transcriptome map:: Clustering of highly expressed genes in chromosomal domains [J].
Caron, H ;
van Schaik, B ;
van der Mee, M ;
Baas, F ;
Riggins, G ;
van Sluis, P ;
Hermus, MC ;
van Asperen, R ;
Boon, K ;
Voûte, PA ;
Heisterkamp, S ;
van Kampen, A ;
Versteeg, R .
SCIENCE, 2001, 291 (5507) :1289-+