GATExplorer (Genomic And Transcriptomic Explorer) is a bioinformatic web platform that integrates a gene loci browser with nucleotide level mappings of oligo probes from expression microarrays. The tool 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 application allows visualization of probes in their genomic context together with any associated protein-coding or non-coding transcripts (i.e. mRNAs and ncRNAs).

To analyze transcriptomic data in a genomic context, GATExplorer integrates five major datasets: (i) the human, mouse and rat genomes (derived from Ensembl); (ii) the sequences and IDs of all oligonucleotide probes (perfect match only) from all Affymetrix (3' and all-exon) expression microarrays for these species; (iii) de novo mapping data of each array probe to the transcriptome of the corresponding organism, with the genomic coordinates for each locus (including locations on exons, introns and along exon-exon junctions) and identification of any intersecting genes, transcripts and exons; (iv) mapping data of unmapped probes to transcripts in RNAdb, a database of ncRNAs of human and mouse; and (v) all expression data derived from a set of microarrays from different cell types, tissues or organs (Gene Expression Atlas) calculated at probe- and probeset-level using the complete de novo mapping.

In this way, GATExplorer web interface provides:
• location and view of each gene locus within the chromosome and chromosomal region
• scaled display of each gene locus with its transcripts structure, including view of the exons and domains
• sequences of the transcripts (cDNAs) and proteins and of the array probes and probesets for each locus
• BLAST tool to find any sequence in the genomic-transcriptomic context
• complete mapping of all oligo probes and probesets from Affymetrix expression microarrays to all known gene loci
• download files (.txt) with the complete mapping of microarray probesets to known genes
• download files (.txt) with the complete mapping of microarray probes to: genes, transcripts, exons, ncRNAs
• R packages (CDFs) to apply the mappings to any specific microarray set using BioConductor
• expression profiles of each gene in a broad set of arrays from different cell types, tissues or organs

The PROBE MAPPING section includes: statistics, methods, comparative analysis, and all the files and packages above-mentioned to use the mappings with any query data set of Affymetrix microarrays. In summary, GATExplorer is an integrated platform that combines genomic visualization with nucleotide-level probe mapping. By considering expression at the nucleotide level rather than the gene level, it provides the means to undertake a higher resolution analysis of microarray data and potentially extract considerably more detailed and biologically interesting information from existing and future microarray experiments.

[Publications related to this work]
Bioinformatics and Functional Genomics Research Group
Cancer Research Center (CiC-IBMCC, CSIC/USAL)
Salamanca - Spain