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In array CGH, because the clones contain sequences information directly connecting with the genome database, array CGH offers rapid genome-wide analysis at high resolution and the information it provides is directly linked to the physical and genetic maps of the human genome.
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SIGMA is a continually expanding database of array CGH experiments.
Raw data were uploaded onto the NCBI GEO Database (The array data has been uploaded onto NCBI GEO database with accession number: GSE51603).
A more detailed annotation file, as well as a database for array data is under development and will be accessible on line [ 6].
All data were entered into a custom-designed database, Expression Array Manager [ 35], and then uploaded into Resolver 5.0 (Rosetta Biosoftware), DecisionSite for Functional Genomics (Spotfire, Inc ., and Ingenuity Pathway Analysis Ingenuity Systemss) for analysis and mining.
This resource has been in operation since 2004 and represents a community driven database of array comparative genomic hybridization (CGH) and WES data that can be used for genomic matchmaking [ 66 ].
Likewise, we identified and imported 215 genes from both published and public databases containing array data and data from other proteomic analyses.
All the probe sets were converted to TIGR MSU Locus IDs in Oligonucleotide rice array database (www.rad.org) and RiceChip database (www.ricechip.com).
We found 134 genes showing correlation between DNA copy number and mRNA expression patterns by integrating our array-CGH database with the expression array databases (Table 4).
Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes.
The availability of integrated genome databases, Affymetrix arrays and mapping populations, coupled to its ease and economy of cultivation have all contributed to the development of Brachypodium as an experimental system for temperate grass biology.
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