GeneSpring GX Analytical Tool
GeneSpring GX Analytical Tool
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Note: This is a review of the published article listed below. All information, quotes, figures, methods, and findings mentioned in this review are from that article, and are the property of its authors and/or the publication in which the article originally appeared.
The magnitude and complexity of genomic data sets make them difficult to interpret, particularly when faced with the rapid technological advances within the microarray industry. Agilent GeneSpring GX is the industry-standard gene expression software tool enabling analysis, comparisons, visualization, and management of gene expression data. Designed to break through bottlenecks in data management and analysis processes, GeneSpring software can import and analyze data from any array source. By combining powerful statistical results with biological relevant annotation information, such as Gene ontologies and pathways, genotype information (in conjunction with GeneSpring GT), the GeneSpring Analysis Platform identifies genes that are truly relevant to your biological question. Charbonnier et al (2005) used the Agilent microarray workflow to design whole-genome oligoarrays, validated for genomotyping, deletion mapping, and gene expression analysis on Staphylococcus aureus. GeneSpring GX enabled the researchers to perform comparative genomic hybridization simply by analyzing with the two-way clustering feature, validating the properties of the custom designed StaphChip.
Figure 1. Mapping of a deleted gene region by StaphChip.
Cy-5 labelled DNA of parental strain SA113 was co-hybridized with Cy-3 labelled DNA from its isogenic ica deletion mutant. Colored bars indicate the position of each probe used to map ica-related and adjacent ORFs. Background signals (green) were recorded from probes recognizing the ica-region known to be deleted in strain SA113ica (arrows), as opposed to positive red signals recorded in the wild-type strain. The tetracycline resistance marker used for the construction and selection of strain SA113ica is recorded in the green channel only. Dye swap experiments provided similar results (not shown). Data are raw signal intensities; background level is indicated by a dotted line.
Figure 2. Comparative genome hybridization using clustering analysis.
Genomic DNA of each individual S. aureus strain was labelled with Cy3 and co-hybridized with equivalent amounts of Cy5-labelled genomic DNA pooled from N315, Mu50 and COL. Background-subtracted data were expressed as Log10 ratios and analyzed by two-way clustering using GeneSpring 6.1. Probes yielding positive and negative signals are shown in blue and yellow, respectively. The significance of black bars (a, b, and c) is indicated in the text. Note that the figure resolution does not allow visualizing single probe differences but only clusters of probes.
Figure 3. Reproducibility of fluorescent signals recorded from multiple non-overlapping capture elements for common transcripts.
10 µg Cy-3 labelled N315 cDNA were hybridized at 60°C on StaphChip. For 2,269 selected transcripts detected by two or multiple probes (n = 5,079), average fluorescence intensities and their maximal relative errors are presented in panel (A), and the cumulative distribution of maximal relative errors in panel (B).
Original Research Paper:
Title: A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus.
Authors: Charbonnier Y, Gettler B, François P, Bento M, Renzoni A, Vaudaux P, Schlegel W, Schrenzel J.
Journal: BMC Genomics. 2005 Jun 17;6:95.
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