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X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

Yates T, Okoniewski MJ, Miller CJ - Nucleic Acids Res. (2007)

Bottom Line: In order to fully exploit these arrays, it is necessary to associate each reporter on the array with the features of the genome it is targeting, and to relate these to gene and genome structure.X:Map is a genome annotation database that provides this information.Data can be browsed using a novel Google-maps based interface, and analysed and further visualized through an associated BioConductor package.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK, Bioinformatics Group, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Withington, Manchester, M20 4BX, UK.

ABSTRACT
Affymetrix exon arrays aim to target every known and predicted exon in the human, mouse or rat genomes, and have reporters that extend beyond protein coding regions to other areas of the transcribed genome. This combination of increased coverage and precision is important because a substantial proportion of protein coding genes are predicted to be alternatively spliced, and because many non-coding genes are known also to be of biological significance. In order to fully exploit these arrays, it is necessary to associate each reporter on the array with the features of the genome it is targeting, and to relate these to gene and genome structure. X:Map is a genome annotation database that provides this information. Data can be browsed using a novel Google-maps based interface, and analysed and further visualized through an associated BioConductor package. The database can be found at http://xmap.picr.man.ac.uk.

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The X:Map build process. (a) Overview. The entire human genome is searched against the array's 25-mer probe sequences by the Java Matching engine. Results are stored in a relational database as a set of additional tables accompanying a local installation of Ensembl. The database is used both by an R client that supports analysis using BioConductor and a webserver that supports a Web 2.0/AJAX Genome Browser. The browser serves a set of pre-computed images generated offline by a coarse-grained parallel task (b). (b) Distributed computation of image tiles using JavaSpaces. Tile generation jobs are placed in a JavaSpace by a master process (Main Java Process). These are consumed by a series of worker processes distributed across a variety of Linux machines. All image data are written to a shared network drive.
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Figure 2: The X:Map build process. (a) Overview. The entire human genome is searched against the array's 25-mer probe sequences by the Java Matching engine. Results are stored in a relational database as a set of additional tables accompanying a local installation of Ensembl. The database is used both by an R client that supports analysis using BioConductor and a webserver that supports a Web 2.0/AJAX Genome Browser. The browser serves a set of pre-computed images generated offline by a coarse-grained parallel task (b). (b) Distributed computation of image tiles using JavaSpaces. Tile generation jobs are placed in a JavaSpace by a master process (Main Java Process). These are consumed by a series of worker processes distributed across a variety of Linux machines. All image data are written to a shared network drive.

Mentions: These data are used to populate a set of new tables in a local copy of Ensembl (11), indexed for speed of querying. An additional set of stored procedures are imported to provide a well-defined API for both the website and the BioConductor package. The Ensembl database does not support foreign keys, but these new tables link to the existing ones using the same unique identifiers as those used by Ensembl. The overall architecture of X:Map is shown in Figure 2a. In total, this phase of the build process takes ∼3 h for Ensembl v45 (human, mouse and rat combined) on a twin-Xeon 64 bit machine with 16 GB RAM running Red Hat Enterprise Linux.Figure 2.


X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

Yates T, Okoniewski MJ, Miller CJ - Nucleic Acids Res. (2007)

The X:Map build process. (a) Overview. The entire human genome is searched against the array's 25-mer probe sequences by the Java Matching engine. Results are stored in a relational database as a set of additional tables accompanying a local installation of Ensembl. The database is used both by an R client that supports analysis using BioConductor and a webserver that supports a Web 2.0/AJAX Genome Browser. The browser serves a set of pre-computed images generated offline by a coarse-grained parallel task (b). (b) Distributed computation of image tiles using JavaSpaces. Tile generation jobs are placed in a JavaSpace by a master process (Main Java Process). These are consumed by a series of worker processes distributed across a variety of Linux machines. All image data are written to a shared network drive.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238884&req=5

Figure 2: The X:Map build process. (a) Overview. The entire human genome is searched against the array's 25-mer probe sequences by the Java Matching engine. Results are stored in a relational database as a set of additional tables accompanying a local installation of Ensembl. The database is used both by an R client that supports analysis using BioConductor and a webserver that supports a Web 2.0/AJAX Genome Browser. The browser serves a set of pre-computed images generated offline by a coarse-grained parallel task (b). (b) Distributed computation of image tiles using JavaSpaces. Tile generation jobs are placed in a JavaSpace by a master process (Main Java Process). These are consumed by a series of worker processes distributed across a variety of Linux machines. All image data are written to a shared network drive.
Mentions: These data are used to populate a set of new tables in a local copy of Ensembl (11), indexed for speed of querying. An additional set of stored procedures are imported to provide a well-defined API for both the website and the BioConductor package. The Ensembl database does not support foreign keys, but these new tables link to the existing ones using the same unique identifiers as those used by Ensembl. The overall architecture of X:Map is shown in Figure 2a. In total, this phase of the build process takes ∼3 h for Ensembl v45 (human, mouse and rat combined) on a twin-Xeon 64 bit machine with 16 GB RAM running Red Hat Enterprise Linux.Figure 2.

Bottom Line: In order to fully exploit these arrays, it is necessary to associate each reporter on the array with the features of the genome it is targeting, and to relate these to gene and genome structure.X:Map is a genome annotation database that provides this information.Data can be browsed using a novel Google-maps based interface, and analysed and further visualized through an associated BioConductor package.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK, Bioinformatics Group, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Withington, Manchester, M20 4BX, UK.

ABSTRACT
Affymetrix exon arrays aim to target every known and predicted exon in the human, mouse or rat genomes, and have reporters that extend beyond protein coding regions to other areas of the transcribed genome. This combination of increased coverage and precision is important because a substantial proportion of protein coding genes are predicted to be alternatively spliced, and because many non-coding genes are known also to be of biological significance. In order to fully exploit these arrays, it is necessary to associate each reporter on the array with the features of the genome it is targeting, and to relate these to gene and genome structure. X:Map is a genome annotation database that provides this information. Data can be browsed using a novel Google-maps based interface, and analysed and further visualized through an associated BioConductor package. The database can be found at http://xmap.picr.man.ac.uk.

Show MeSH