Microarray
PROBE MAPPING
Sequence alignment tool (BLAST) is used to build the complete mappings of all oligonucleotide probes from Affymetrix expression microarrays to the current versions of human, mouse and rat transcriptomes. The mappings are done for the probes of the popular GeneChip 3' expression microarrays (e.g. human HG_U133A) and the new all-exon expression microarrays (e.g. Human_Gene_1.0 and Human_Exon_1.0). Complete de novo mapping data of each array probe to the transcriptome of the corresponding organism, with the genomic coordinates (Ensembl) for each locus (including locations on exons, introns and along exon-exon junctions) and identification of any intersecting genes, transcripts and exons are provided. Moreover, the probes which did not map on any protein-coding region are re-mapped to a specific database of non-coding RNAs (ncRNAs) for human and mouse (RNAdb).

Genome-wide, updated and unambiguous mapping of all probes from expression microarrays to all known transcribed entities of a functional genome (i.e. genes, transcripts, exons and ncRNAs) is needed to undertake a higher resolution analysis of microarray data and potentially extract considerably more detailed and biologically interesting information from microarray experiments.

In order to enable the use of the mappings this section includes the following files to be downloaded:

text files (.txt) with complete unambiguous mapping of the microarray probesets to genes (probesets2genes)
text files (.txt) with complete unambiguous mapping of microarray probes to genes (probes2genes)
text files (.txt) with complete unambiguous mapping of microarray probes to transcripts (probes2transcripts)
text files (.txt) with mapping of the probes that are ambiguous because they map on more than one gene locus (ambigprobes2genes)
text files (.txt) with complete unambiguous mapping of microarray probes to genes plus a detailed complete mapping to transcripts (probes2genesplustranscripts)

• R chip definition files (CDFs) with complete unambiguous mapping of microarray probes to genes (GeneMapper)
• R chip definition files (CDFs) with complete unambiguous mapping of microarray probes to transcripts (TranscriptMapper)
• R chip definition files (CDFs) with complete unambiguous mapping of microarray probes to exons (ExonMapper)
• R chip definition files (CDFs) with mapping to ncRNAs of the probes that did not map any known protein-coding exon (ncRNA Mapper)

annotation files with information about the mapped entities: genes, transcripts and exons.
annotation files that include only selected subsets of the protein-coding genes or of the miRNAs.

The probes that only map on introns (visualized in GATExplorer web application) are included in the ncRNA Mapper package only if they are assigned to a specific non-coding RNA from RNAdb.

Comparative Analysis of GATExplorer with other published related applications is included in the last part of this section. We also present there a practical example of the use of GeneMapper to show that complete and unambiguous mapping of the oligo probes from expression microarrays to the currently known gene-set of a given organism provides a clear improvement in the expression calculations. The comparison is presented for a dataset of mouse micorarrays analysed using four different procedures, including a comparison of RMA with standard Affymetrix CDFs versus RMA with the CDFs provided by GATExplorer.