Characterization of a Human Fovea cDNA Library and Regional Differential Gene Expression in the Human Retina

Bernstein, Steven L.; Borst, Diane E.; Neuder, Michelle E.; Wong, Paul

doi:10.1006/geno.1996.0123

Cited by 40 publications

(23 citation statements)

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“…The same bias applies to the SAGE technique which, in addition, is affected by an underestimation of the very abundant transcripts. In the present study, the genes represented by one or two ESTs over 24,802 were considered as rare, whereas previous studies (Bernstein et al 1996;Shimitsu-Matsumoto et al 1997;Maeda et al 1997) reported as rare those genes represented by a single EST over ∼1000. As the number of molecules of Cold Spring Harbor Laboratory Press on May 11, 2018 -Published by genome.cshlp.org Downloaded from mRNA per nucleus is ∼150,000, a given transcript with a concentration of 10 molecules per nucleus would have about an 18% chance of remaining undetected in a sample of 25,000 ESTs.…”

Section: Discussioncontrasting

confidence: 61%

“…The basic assumption is that the larger the number of skeletal muscle ESTs reported per entry, the more active the corresponding gene in the tissue. The number of ESTs per entry represents the best available estimate of the abundance of each individual transcript in the skeletal muscle mRNA population (Okubo et al 1992;Itoh et al 1994Itoh et al , 1998Bernstein et al 1996;Hwang et al 1997;Maeda et al 1997;Bortoluzzi et al 1998).…”

Section: Methodsmentioning

confidence: 99%

“…Preliminary analysis of collections of genes expressed in specific human tissues has been reported previously (Okubo et al 1992;Itoh et al 1994Itoh et al , 1998Bernstein et al 1996;Hwang et al 1997;Maeda et al 1997;Shimizu-Matsumoto et al 1997;Bortoluzzi et al 1998;Itoh et al 1998). Expression profiles of human skeletal muscle involving <1000 genes have been produced in the past (Pietu et al 1996;Lanfranchi et al 1996).…”

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confidence: 99%

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The Human Adult Skeletal Muscle Transcriptional Profile Reconstructed by a Novel Computational Approach

Bortoluzzi

d’Alessi²,

Romualdi³

et al. 2000

Genome Res.

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By applying a novel software tool, information on 4080 UniGene clusters was retrieved from three adult human skeletal muscle cDNA libraries, which were selected for being neither normalized nor subtracted. Reconstruction of a transcriptional profile of the corresponding tissue was attempted by a computational approach, classifying each transcript according to its level of expression. About 25% of the transcripts accounted for about 80% of the detected transcriptional activity, whereas most genes showed a low level of expression. This in silico transcriptional profile was then compared with data obtained by a SAGE study. A fairly good agreement between the two methods was observed. About 400 genes, highly expressed in skeletal muscle or putatively skeletal muscle-specific, may represent the minimal set of genes needed to determine the tissue specificity. These genes could be used as a convenient reference to monitor major changes in the transcriptional profile of adult human skeletal muscle in response to different physiological or pathological conditions, thus providing a framework for designing DNA microarrays and initiating biological studies.Preliminary analysis of collections of genes expressed in specific human tissues has been reported previously

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Section: Discussioncontrasting

confidence: 61%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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The Human Adult Skeletal Muscle Transcriptional Profile Reconstructed by a Novel Computational Approach

Bortoluzzi

d’Alessi²,

Romualdi³

et al. 2000

Genome Res.

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“…This process involves different types of retinal cells, mainly neuronal cells (e.g., photoreceptors, bipolar cells, and others) and the nonneuronal retinal pigment epithelium (RPE). The set of genes expressed by the human neural retina has been elucidated partially, mainly through reported expressed sequence tag (EST) libraries [nonnormalized (1)(2)(3) or enriched (4, 5)] that contain over 16,000 EST sequences derived from less than 5,000 genes (6). Our knowledge of the set of genes expressed by the RPE is more rudimentary, because only 624 ESTs have been sequenced (refs.…”

mentioning

confidence: 99%

“…4 and 7, and GenBank Library 6359). Little is known about the variation in gene expression between different regions of the retina (e.g., the retinal periphery versus the macula); only a few genes with a preferential expression in the fovea have been identified (1). There is no counterpart to these different retinal regions in mouse retinas.…”

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confidence: 99%

Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE)

Sharon

Blackshaw

Cepko

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

146

120

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We used the serial analysis of gene expression (SAGE) technique to catalogue and measure the relative levels of expression of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium (RPE) from one or both of two humans, aged 88 and 44 years. The cone photoreceptor contribution to all transcription in the retina was found to be similar in the macula versus the retinal periphery, whereas the rod contribution was greater in the periphery versus the macula. Genes encoding structural proteins for axons were found to be expressed at higher levels in the macula versus the retinal periphery, probably reflecting the large proportion of ganglion cells in the central retina. In comparison with the younger eye, the peripheral retina of the older eye had a substantially higher proportion of mRNAs from genes encoding proteins involved in iron metabolism or protection against oxidative damage and a substantially lower proportion of mRNAs from genes encoding proteins involved in rod phototransduction. These differences may reflect the difference in age between the two donors or merely interindividual variation. The RPE library had numerous previously unencountered tags, suggesting that this cell type has a large, idiosyncratic repertoire of expressed genes. Comparison of these libraries with 100 reported nonocular SAGE libraries revealed 89 retina-specific or enriched genes expressed at substantial levels, of which 14 are known to cause a retinal disease and 53 are RPE-specific genes. We expect that these libraries will serve as a resource for understanding the relative expression levels of genes in the retina and the RPE and for identifying additional disease genes. T he human retina is a highly specialized tissue that converts photons into neural signals that are communicated to the brain. This process involves different types of retinal cells, mainly neuronal cells (e.g., photoreceptors, bipolar cells, and others) and the nonneuronal retinal pigment epithelium (RPE). The set of genes expressed by the human neural retina has been elucidated partially, mainly through reported expressed sequence tag (EST) libraries [nonnormalized (1-3) or enriched (4, 5)] that contain over 16,000 EST sequences derived from less than 5,000 genes (6). Our knowledge of the set of genes expressed by the RPE is more rudimentary, because only 624 ESTs have been sequenced (refs. 4 and 7, and GenBank Library 6359). Little is known about the variation in gene expression between different regions of the retina (e.g., the retinal periphery versus the macula); only a few genes with a preferential expression in the fovea have been identified (1). There is no counterpart to these different retinal regions in mouse retinas. Knowledge of the set of genes expressed in these regions is valuable, because some common diseases of the retina can affect one region preferentially (e.g., age-related macular degeneration).The serial analysis of gene expression (SAGE) procedure, first described by Velculescu et al. (8), allows the comp...

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Isolation and Mapping of Novel Candidate Genes for Retinal Disorders Using Suppression Subtractive Hybridization

et al. 1999

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Characterization of a Human Fovea cDNA Library and Regional Differential Gene Expression in the Human Retina

Cited by 40 publications

References 0 publications

The Human Adult Skeletal Muscle Transcriptional Profile Reconstructed by a Novel Computational Approach

The Human Adult Skeletal Muscle Transcriptional Profile Reconstructed by a Novel Computational Approach

Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE)

Isolation and Mapping of Novel Candidate Genes for Retinal Disorders Using Suppression Subtractive Hybridization

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