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GATExplorer specifications

Information


Unique identifier OMICS_18345
Name GATExplorer
Alternative name Genomic and Transcriptomic Explorer
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No

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Publications for Genomic and Transcriptomic Explorer

GATExplorer citations

 (7)
library_books

Mining, Validation, and Clinical Significance of Colorectal Cancer (CRC) Associated lncRNAs

2016
PLoS One
PMCID: 5082825
PMID: 27788162
DOI: 10.1371/journal.pone.0164590

[…] rous and paracancerous samples per group. IQRray_score [] and presence/absence call [] were used to ensure the overall quality of microarray data and exclude any abnormal specimens. A platform called GATExplorer [] was used to analyze microarray data at the nucleotide level in a genomic context and distinguish lncRNA candidates.The standards for lncRNAs in GATExplorer were:(i) there was experiment […]

library_books

A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples

2014
BMC Genomics
PMCID: 4298068
PMID: 25297679
DOI: 10.1186/1471-2164-15-879

[…] ping of all probes to the currently known expressed biological entities, i.e. to the known human protein-coding gene loci and to each specific exon defined on the loci (taking the mapping provided by GATExplorer) []. Exon junction probes are not considered in this study for two reasons: (i) the generation of exon arrays that we are analyzing are no designed to have exon-exon junction probes becaus […]

library_books

A four long non coding RNA signature in predicting breast cancer survival

2014
PMCID: 4198622
PMID: 25288503
DOI: 10.1186/s13046-014-0084-7

[…] The raw CEL files were downloaded from GEO database and background adjusted using Robust Multichip Average. GATExplorer [] was used to process microarrays on a local computer for gene expressions of lncRNAs. This GATExplorer provides a series of R packages, designed to be used with BioConductor tools, that […]

library_books

Transcriptome meta analysis reveals a central role for sex steroids in the degeneration of hippocampal neurons in Alzheimer’s disease

2013
BMC Syst Biol
PMCID: 3702487
PMID: 23803348
DOI: 10.1186/1752-0509-7-51

[…] open source Bioconductor bioinformatics software, http://www.bioconductor.org). In the uploading process CDF files were associated with the microarrays through the GeneMapper package. Downloaded from GATExplorer [-] GeneMapper (http://bioinfow.dep.usal.es/xgate/mapping/mapping.php) includes the sets of unambiguous probes that map to each specific Ensemble Gene ID (ENSG ID). Also through affy packa […]

library_books

Molecular Characterization of Chronic Lymphocytic Leukemia Patients with a High Number of Losses in 13q14

2012
PLoS One
PMCID: 3496725
PMID: 23152777
DOI: 10.1371/journal.pone.0048485

[…] on . The absolute expression signal for each gene was calculated for each microarray. For the expression signal calculation of the Human Exon arrays we used a new CDF package, called GeneMapper (from GATExplorer) , instead of the Affymetrix original probe-set definition. This mapping represents an improvement thanks to the reannotation of updated Ensembl gene loci and removal of cross-hybridizatio […]

library_books

Gene expression profiling of peripheral blood mononuclear cells in the setting of peripheral arterial disease

2012
J Clin Bioinforma
PMCID: 3381689
PMID: 22409835
DOI: 10.1186/2043-9113-2-6

[…] 05; ) (Table ). A subset of probes was not annotated in Affymetrix annotation files. We obtained enhanced probe mapping by combining results from multiple probe mapping tools AILUN [], BioMart [] and GATExplorer []. Final probe mapping was performed using the union of mapped results obtained from these methods. NCBI-Gene and UCSC genome browser [] were also consulted for annotation and integration […]

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GATExplorer institution(s)
Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Salamanca, Spain; Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
GATExplorer funding source(s)
Supported by the spanish Ministry of Science and Innovation MICINN (ISCiii, ref. projects PI061153 and PS09/00843) and the local government Junta de Castilla y León (ref. projects CSI03A06 and CSI07A09).

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