| Methods |
This page provides a graphical view of the main data sources and methods included in
GATExplorer. The graph bellow shows the pipeline followed to build GATExplorer
database and web platform and the files and packages provided by this server.
It can be seen that the main external databases are:
Ensembl,
RNAdb,
Affymetrix and
Gene Atlas.
BLASTN sequence alignment tool was used to map the 25-mer oligo probes of the main
Affymetrix expression microarrays to the RNA sequences of human, mouse and
rat, selecting only complete perfect match alignments.
The source sequence databases for these RNAs were: Ensembl for protein-coding RNAs
(mRNAs / cDNAs) and Ensembl plus RNAdb for non protein-coding RNAs (ncRNAs).
After the mapping, the probes were placed in the context of each genome
following the genomic coordinates of the main entities defined by Ensembl.
In this way, GATExplorer allows integrated exploration of any gene loci within these
genomes, presenting the genes, transcripts and exons with the probes
that map on each one, plus data about their expression in a set of microarrays samples from
different cells/tissues/organs (derived from Gene Atlas).
The PROBE MAPPING data included in GATExplorer for each microarray
is ready to download and it can be used to obtain an accurate expression profiling
for either genes, transcripts, exons or ncRNAs.
R and
BioConductor
packages and tools are provided to achieve the microarray expression signal calculation
according to these de novo mapping. |
| GATExplorer pipeline |
 |
|
|
