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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

Typical library summary page. This Web page displays the analyzed EST data from a lens-derived cDNA library. Clones are ranked in order of abundance but can also be displayed and sorted by chromosomal location or by functional keyword (GO terms).
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f3: Typical library summary page. This Web page displays the analyzed EST data from a lens-derived cDNA library. Clones are ranked in order of abundance but can also be displayed and sorted by chromosomal location or by functional keyword (GO terms).

Mentions: NEIBank generates web pages for each of the GRIST-analyzed cDNA libraries. These can be accessed from the home page (Figure 2), which has an image of the human eye and hyperlinks and text links to data for different eye tissues and species. Each library page has a common format (Figure 3). The first line provides the library name and description including the source of the cDNA, the species, the tissue, and, for NEIBank-generated cDNA libraries, a letter code (such as by or he, derived from the high throughput sequencing pipeline) that catalogs the libraries or sublibraries included. The next row provides references and links to publications describing library construction and analysis. The table header also provides user-selectable options for sorting, viewing, and formatting the data table. The default web page view of each EST collection is organized according to the abundance of clones in each group in descending order. For each cluster of clones, there is a description field that contains two identifiers: one derived from RefSeq (or GenBank NR) matches and the other from UniGene matches. While RefSeq/NR and UniGene identifications usually agree, this is not always the case. Including independent assignments of identity increases the chances of finding more informative names and also reveals potential issues arising from undetected chimeras or from overlapping genes.


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)

Typical library summary page. This Web page displays the analyzed EST data from a lens-derived cDNA library. Clones are ranked in order of abundance but can also be displayed and sorted by chromosomal location or by functional keyword (GO terms).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Typical library summary page. This Web page displays the analyzed EST data from a lens-derived cDNA library. Clones are ranked in order of abundance but can also be displayed and sorted by chromosomal location or by functional keyword (GO terms).
Mentions: NEIBank generates web pages for each of the GRIST-analyzed cDNA libraries. These can be accessed from the home page (Figure 2), which has an image of the human eye and hyperlinks and text links to data for different eye tissues and species. Each library page has a common format (Figure 3). The first line provides the library name and description including the source of the cDNA, the species, the tissue, and, for NEIBank-generated cDNA libraries, a letter code (such as by or he, derived from the high throughput sequencing pipeline) that catalogs the libraries or sublibraries included. The next row provides references and links to publications describing library construction and analysis. The table header also provides user-selectable options for sorting, viewing, and formatting the data table. The default web page view of each EST collection is organized according to the abundance of clones in each group in descending order. For each cluster of clones, there is a description field that contains two identifiers: one derived from RefSeq (or GenBank NR) matches and the other from UniGene matches. While RefSeq/NR and UniGene identifications usually agree, this is not always the case. Including independent assignments of identity increases the chances of finding more informative names and also reveals potential issues arising from undetected chimeras or from overlapping genes.

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