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arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays.

Menten B, Pattyn F, De Preter K, Robbrecht P, Michels E, Buysse K, Mortier G, De Paepe A, van Vooren S, Vermeesch J, Moreau Y, De Moor B, Vermeulen S, Speleman F, Vandesompele J - BMC Bioinformatics (2005)

Bottom Line: We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format.Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms.ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium. bjorn.menten@ugent.be <bjorn.menten@ugent.be>

ABSTRACT

Background: The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment.

Results: We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser.

Conclusion: ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

Show MeSH
Quality control graphs. Graphical displays to assess the quality of an experiment, such as a dual channel intensity scatter plot, ratio histogram, ratio-intensity plot and a virtual slide view.
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Figure 2: Quality control graphs. Graphical displays to assess the quality of an experiment, such as a dual channel intensity scatter plot, ratio histogram, ratio-intensity plot and a virtual slide view.

Mentions: In addition to these parameters, different graphical displays, such as ratio-intensity plots (usually referred to as MA plots), dual channel intensity scatter plots, and ratio histograms give an idea of the quality of an individual experiment or series of experiments (Figure 2). In all these visualizations, thresholds for gains and losses are displayed and can be adjusted. The slide viewer generates a virtual spatial view of all features on the array using the ratio, or signal and background intensities; this viewer allows the identification of problematic regions or artifacts on the slide surface. Clicking on an individual feature shows specific data associated with this feature (e.g., reporter name, signal intensities, and data quality flags).


arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays.

Menten B, Pattyn F, De Preter K, Robbrecht P, Michels E, Buysse K, Mortier G, De Paepe A, van Vooren S, Vermeesch J, Moreau Y, De Moor B, Vermeulen S, Speleman F, Vandesompele J - BMC Bioinformatics (2005)

Quality control graphs. Graphical displays to assess the quality of an experiment, such as a dual channel intensity scatter plot, ratio histogram, ratio-intensity plot and a virtual slide view.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1173083&req=5

Figure 2: Quality control graphs. Graphical displays to assess the quality of an experiment, such as a dual channel intensity scatter plot, ratio histogram, ratio-intensity plot and a virtual slide view.
Mentions: In addition to these parameters, different graphical displays, such as ratio-intensity plots (usually referred to as MA plots), dual channel intensity scatter plots, and ratio histograms give an idea of the quality of an individual experiment or series of experiments (Figure 2). In all these visualizations, thresholds for gains and losses are displayed and can be adjusted. The slide viewer generates a virtual spatial view of all features on the array using the ratio, or signal and background intensities; this viewer allows the identification of problematic regions or artifacts on the slide surface. Clicking on an individual feature shows specific data associated with this feature (e.g., reporter name, signal intensities, and data quality flags).

Bottom Line: We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format.Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms.ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium. bjorn.menten@ugent.be <bjorn.menten@ugent.be>

ABSTRACT

Background: The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment.

Results: We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser.

Conclusion: ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

Show MeSH