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NEIBank: genomics and bioinformatics resources for vision research.

Wistow G, Peterson K, Gao J, Buchoff P, Jaworski C, Bowes-Rickman C, Ebright JN, Hauser MA, Hoover D - Mol. Vis. (2008)

Bottom Line: NEIBank is an integrated resource for genomics and bioinformatics in vision research.All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser.NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology.

View Article: PubMed Central - PubMed

Affiliation: Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-0703, USA. graeme@helix.nih.gov

ABSTRACT
NEIBank is an integrated resource for genomics and bioinformatics in vision research. It includes expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology.

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Related in: MedlinePlus

Detail of EyeBrowse view of ESTs for the human NRL gene. ESTs for NRL from human retina are shown aligned with the RefSeq gene. The red asterisk highlights a group of three cDNAs, all of which contain an alternative exon with a potential protein coding open reading frame. Note, also, there are several ESTs from a longer 3′ UTR of the gene that do not overlap with the RefSeq sequence.
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f5: Detail of EyeBrowse view of ESTs for the human NRL gene. ESTs for NRL from human retina are shown aligned with the RefSeq gene. The red asterisk highlights a group of three cDNAs, all of which contain an alternative exon with a potential protein coding open reading frame. Note, also, there are several ESTs from a longer 3′ UTR of the gene that do not overlap with the RefSeq sequence.

Mentions: EyeBrowse displays EST data tracks specifically for eye-derived cDNA libraries, organized by tissue (for example, human lens or retina). In addition to human, EyeBrowse hosts data for all species for which both eye EST and genome sequence are available through the UCSC genome builds; currently this includes mouse, rat, dog, cow, rhesus monkey, chicken, and zebrafish. EyeBrowse thus provides a convenient way to display all the known eye-expressed ESTs in and around a particular gene. This provides a rapid graphical overview of EST-based expression patterns and alternative transcripts for particular genes and allows easy identification of potential full-length clones for expression studies. For example, Figure 5 shows human retina EST data for the important retinal transcription factor NRL [37]. The asterisk indicates three aligned clones for an alternative transcript of this gene using an additional exon. The alternative exon contains an open reading frame and is also observed in the orthologous mouse gene (not shown), suggesting that it may have functional significance [2,4].


NEIBank: genomics and bioinformatics resources for vision research.

Wistow G, Peterson K, Gao J, Buchoff P, Jaworski C, Bowes-Rickman C, Ebright JN, Hauser MA, Hoover D - Mol. Vis. (2008)

Detail of EyeBrowse view of ESTs for the human NRL gene. ESTs for NRL from human retina are shown aligned with the RefSeq gene. The red asterisk highlights a group of three cDNAs, all of which contain an alternative exon with a potential protein coding open reading frame. Note, also, there are several ESTs from a longer 3′ UTR of the gene that do not overlap with the RefSeq sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2480482&req=5

f5: Detail of EyeBrowse view of ESTs for the human NRL gene. ESTs for NRL from human retina are shown aligned with the RefSeq gene. The red asterisk highlights a group of three cDNAs, all of which contain an alternative exon with a potential protein coding open reading frame. Note, also, there are several ESTs from a longer 3′ UTR of the gene that do not overlap with the RefSeq sequence.
Mentions: EyeBrowse displays EST data tracks specifically for eye-derived cDNA libraries, organized by tissue (for example, human lens or retina). In addition to human, EyeBrowse hosts data for all species for which both eye EST and genome sequence are available through the UCSC genome builds; currently this includes mouse, rat, dog, cow, rhesus monkey, chicken, and zebrafish. EyeBrowse thus provides a convenient way to display all the known eye-expressed ESTs in and around a particular gene. This provides a rapid graphical overview of EST-based expression patterns and alternative transcripts for particular genes and allows easy identification of potential full-length clones for expression studies. For example, Figure 5 shows human retina EST data for the important retinal transcription factor NRL [37]. The asterisk indicates three aligned clones for an alternative transcript of this gene using an additional exon. The alternative exon contains an open reading frame and is also observed in the orthologous mouse gene (not shown), suggesting that it may have functional significance [2,4].

Bottom Line: NEIBank is an integrated resource for genomics and bioinformatics in vision research.All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser.NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology.

View Article: PubMed Central - PubMed

Affiliation: Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-0703, USA. graeme@helix.nih.gov

ABSTRACT
NEIBank is an integrated resource for genomics and bioinformatics in vision research. It includes expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology.

Show MeSH
Related in: MedlinePlus