GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

Abstract

BackgroundGenome-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.ResultsGATExplorer (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).ConclusionsGATExplorer 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.

Dysregulation of long non-coding RNA profiles in human colorectal cancer and its association with overall survival

“…In a previous study, each of the four probes designed to match a gene represented the expression of the gene (13). Various other microarray-based platforms could also be re-annotated for lncRNAs, such as Affymetrix U133A (21,22 (23,24). That was the reason why these datasets were collected from previous studies based on the Affymetrix Exon 1.0 ST Array.…”

Potential prognostic long non-coding RNA identification and their validation in predicting survival of patients with multiple myeloma

“…Genomic and Transcriptomic Explorer (GATExplorer), a database and web platform integrating a gene loci browser with nucleotide level mappings of oligo probes from expression microarrays, 25 was applied to visualize probes in Affymetrix HG U133 Plus 2.0 together with any lncRNAs. With a series of files and packages (R chip definition files (CDFs)) provided by this platform to analyze particular query expression datasets, certain annotation information was available using affy package in Bioconductor (http:// www.bioconductor.org/packages/release/bioc/html/affy.…”

Elevated expression of protein arginine methyltransferase 5 predicts the poor prognosis of breast cancer

“…The raw CEL files were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/), and the background was adjusted according to the previously described method. 26 The expression of PRMT5 was dichotomized using study-specific median expression as the cutoff to define "high value" as above the median versus "low value" as below the median. The Kaplan-Meier method and log-rank test were performed to show survival differences according to PRMT5 expression.…”