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GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs.

Risueño A, Fontanillo C, Dinger ME, De Las Rivas J - BMC Bioinformatics (2010)

Bottom Line: Moreover, as our knowledge of metazoan genomes improves, the number of both protein-coding and noncoding genes, as well as their associated isoforms, continues to increase.By considering expression at the nucleotide level rather than the gene level, it shows that the arrays detect expression signals from entities that most researchers do not contemplate or discriminate.This approach provides the means to undertake a higher resolution analysis of microarray data and potentially extract considerably more detailed and biologically accurate information from existing and future microarray experiments.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Salamanca, Spain.

ABSTRACT

Background: Genome-wide expression studies have developed exponentially in recent years as a result of extensive use of microarray technology. However, expression signals are typically calculated using the assignment of "probesets" to genes, without addressing the problem of "gene" definition or proper consideration of the location of the measuring probes in the context of the currently known genomes and transcriptomes. Moreover, as our knowledge of metazoan genomes improves, the number of both protein-coding and noncoding genes, as well as their associated isoforms, continues to increase. Consequently, there is a need for new databases that combine genomic and transcriptomic information and provide updated mapping of expression probes to current genomic annotations.

Results: GATExplorer (Genomic and Transcriptomic Explorer) is a database and web platform that integrates a gene loci browser with nucleotide level mappings of oligo probes from expression microarrays. It allows interactive exploration of gene loci, transcripts and exons of human, mouse and rat genomes, and shows the specific location of all mappable Affymetrix microarray probes and their respective expression levels in a broad set of biological samples. The web site allows visualization of probes in their genomic context together with any associated protein-coding or noncoding transcripts. In the case of all-exon arrays, this provides a means by which the expression of the individual exons within a gene can be compared, thereby facilitating the identification and analysis of alternatively spliced exons. The application integrates data from four major source databases: Ensembl, RNAdb, Affymetrix and GeneAtlas; and it provides the users with a series of files and packages (R CDFs) to analyze particular query expression datasets. The maps cover both the widely used Affymetrix GeneChip microarrays based on 3' expression (e.g. human HG U133 series) and the all-exon expression microarrays (Gene 1.0 and Exon 1.0).

Conclusions: GATExplorer is an integrated database that combines genomic/transcriptomic visualization with nucleotide-level probe mapping. By considering expression at the nucleotide level rather than the gene level, it shows that the arrays detect expression signals from entities that most researchers do not contemplate or discriminate. This approach provides the means to undertake a higher resolution analysis of microarray data and potentially extract considerably more detailed and biologically accurate information from existing and future microarray experiments.

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Related in: MedlinePlus

Graphical view of the pipeline followed to build the GATExplorer application, showing the data sources integrated (Ensembl, RNAdb, Affymetrix and GeneAtlas -i.e. the four external databases marked in blue square frames-) and a schematic view of the main methods applied at each step -marked with grey gears. As a result, the outputs from the pipeline provide the web platform, which encloses several inhouse built databases -marked in yellow square frames- and several data and tools -marked in orange-, including the files (Text files) and packages (R CDFs) with the de novo mapping of the array probes to the transcriptome of the corresponding organism (human, mouse or rat). The application also provides the genomic coordinates to each locus (including mapping on exons, introns and along exon-exon junctions) and identification of any intersecting genes, transcripts, exons and ncRNAs.
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Figure 1: Graphical view of the pipeline followed to build the GATExplorer application, showing the data sources integrated (Ensembl, RNAdb, Affymetrix and GeneAtlas -i.e. the four external databases marked in blue square frames-) and a schematic view of the main methods applied at each step -marked with grey gears. As a result, the outputs from the pipeline provide the web platform, which encloses several inhouse built databases -marked in yellow square frames- and several data and tools -marked in orange-, including the files (Text files) and packages (R CDFs) with the de novo mapping of the array probes to the transcriptome of the corresponding organism (human, mouse or rat). The application also provides the genomic coordinates to each locus (including mapping on exons, introns and along exon-exon junctions) and identification of any intersecting genes, transcripts, exons and ncRNAs.

Mentions: Figure 1 presents a graphical view of the main data sources and methods included in GATExplorer described above. The graph shows the pipeline followed to build the database and web platform. The probe mapping files (Text files) and packages (R CDFs) are freely provided as part of the repository to allow researchers to use the microarray probe remapping data for their own expression analyses.


GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs.

Risueño A, Fontanillo C, Dinger ME, De Las Rivas J - BMC Bioinformatics (2010)

Graphical view of the pipeline followed to build the GATExplorer application, showing the data sources integrated (Ensembl, RNAdb, Affymetrix and GeneAtlas -i.e. the four external databases marked in blue square frames-) and a schematic view of the main methods applied at each step -marked with grey gears. As a result, the outputs from the pipeline provide the web platform, which encloses several inhouse built databases -marked in yellow square frames- and several data and tools -marked in orange-, including the files (Text files) and packages (R CDFs) with the de novo mapping of the array probes to the transcriptome of the corresponding organism (human, mouse or rat). The application also provides the genomic coordinates to each locus (including mapping on exons, introns and along exon-exon junctions) and identification of any intersecting genes, transcripts, exons and ncRNAs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875241&req=5

Figure 1: Graphical view of the pipeline followed to build the GATExplorer application, showing the data sources integrated (Ensembl, RNAdb, Affymetrix and GeneAtlas -i.e. the four external databases marked in blue square frames-) and a schematic view of the main methods applied at each step -marked with grey gears. As a result, the outputs from the pipeline provide the web platform, which encloses several inhouse built databases -marked in yellow square frames- and several data and tools -marked in orange-, including the files (Text files) and packages (R CDFs) with the de novo mapping of the array probes to the transcriptome of the corresponding organism (human, mouse or rat). The application also provides the genomic coordinates to each locus (including mapping on exons, introns and along exon-exon junctions) and identification of any intersecting genes, transcripts, exons and ncRNAs.
Mentions: Figure 1 presents a graphical view of the main data sources and methods included in GATExplorer described above. The graph shows the pipeline followed to build the database and web platform. The probe mapping files (Text files) and packages (R CDFs) are freely provided as part of the repository to allow researchers to use the microarray probe remapping data for their own expression analyses.

Bottom Line: Moreover, as our knowledge of metazoan genomes improves, the number of both protein-coding and noncoding genes, as well as their associated isoforms, continues to increase.By considering expression at the nucleotide level rather than the gene level, it shows that the arrays detect expression signals from entities that most researchers do not contemplate or discriminate.This approach provides the means to undertake a higher resolution analysis of microarray data and potentially extract considerably more detailed and biologically accurate information from existing and future microarray experiments.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Salamanca, Spain.

ABSTRACT

Background: Genome-wide expression studies have developed exponentially in recent years as a result of extensive use of microarray technology. However, expression signals are typically calculated using the assignment of "probesets" to genes, without addressing the problem of "gene" definition or proper consideration of the location of the measuring probes in the context of the currently known genomes and transcriptomes. Moreover, as our knowledge of metazoan genomes improves, the number of both protein-coding and noncoding genes, as well as their associated isoforms, continues to increase. Consequently, there is a need for new databases that combine genomic and transcriptomic information and provide updated mapping of expression probes to current genomic annotations.

Results: GATExplorer (Genomic and Transcriptomic Explorer) is a database and web platform that integrates a gene loci browser with nucleotide level mappings of oligo probes from expression microarrays. It allows interactive exploration of gene loci, transcripts and exons of human, mouse and rat genomes, and shows the specific location of all mappable Affymetrix microarray probes and their respective expression levels in a broad set of biological samples. The web site allows visualization of probes in their genomic context together with any associated protein-coding or noncoding transcripts. In the case of all-exon arrays, this provides a means by which the expression of the individual exons within a gene can be compared, thereby facilitating the identification and analysis of alternatively spliced exons. The application integrates data from four major source databases: Ensembl, RNAdb, Affymetrix and GeneAtlas; and it provides the users with a series of files and packages (R CDFs) to analyze particular query expression datasets. The maps cover both the widely used Affymetrix GeneChip microarrays based on 3' expression (e.g. human HG U133 series) and the all-exon expression microarrays (Gene 1.0 and Exon 1.0).

Conclusions: GATExplorer is an integrated database that combines genomic/transcriptomic visualization with nucleotide-level probe mapping. By considering expression at the nucleotide level rather than the gene level, it shows that the arrays detect expression signals from entities that most researchers do not contemplate or discriminate. This approach provides the means to undertake a higher resolution analysis of microarray data and potentially extract considerably more detailed and biologically accurate information from existing and future microarray experiments.

Show MeSH
Related in: MedlinePlus