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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/.

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arrayCGHbase scheme. The data is stored in a MIAME supportive MySQL database (red) and reporter info is updated using the NCBI, Ensembl and UCSC genome database. Data and results are presented to the user through a web browser via the PHP scripting language. Data-normalization and other analysis or result visualization methods can be integrated using the plug-in architecture. Further data processing using the R statistical scripting language will be implemented in the near future. Results can be exported to a Progenetix or MIAME compatible format, or visualized on the genome using the Ensemble or UCSC genome browser.
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Figure 1: arrayCGHbase scheme. The data is stored in a MIAME supportive MySQL database (red) and reporter info is updated using the NCBI, Ensembl and UCSC genome database. Data and results are presented to the user through a web browser via the PHP scripting language. Data-normalization and other analysis or result visualization methods can be integrated using the plug-in architecture. Further data processing using the R statistical scripting language will be implemented in the near future. Results can be exported to a Progenetix or MIAME compatible format, or visualized on the genome using the Ensemble or UCSC genome browser.

Mentions: arrayCGHbase runs in Windows, Linux, Macintosh, and Unix environments. Particular attention was paid to the use of open source software for the development of arrayCGHbase. The software was developed in the PHP scripting language, with all data being stored in a relational, MIAME [8] (Minimal Information About a Microarray Experiment) supportive, MySQL database and communicated to the user through an Apache Web server (Figure 1). After installation on a private server, experiments can be shared by different users over the internet or a local intranet. ArrayCGHbase integrates DNA sample information, lab protocols, extracted data, and contains a plug-in architecture for data transformation, analysis, and graphical display, allowing users to develop their own modules. Reporters can be directly linked to the Ensembl [9] or UCSC [10] genome browsers, providing additional up-to-date information on each reporter. Reporters can also be manually imported into the MySQL database with the ability to update all linked experiments. The structure of arrayCGHbase was designed to follow the laboratory workflow and is compatible with all types of arrayCGH experiments and data formats (dual colour genomic clone, cDNA [11], or oligonucleotide [12] arrays spotted on any substrate, physical layout, type of array, as well as single channel hybridizations such as the Affymetrix SNP chips [13]). With a personal account and administrated access levels, a user can enter new DNA samples, annotate these, and append all relevant sample information such as quantity, quality, and applied lab protocols at each step. Each user can group experiments together into projects and, in a uniform and streamlined fashion, apply filters and transformations and run analyses. Data is exportable in several formats for offline analysis using other (dedicated) software tools, for publication or for sharing data with the research community. For advanced users, an SQL query window allows interrogation of the underlying MySQL database.


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)

arrayCGHbase scheme. The data is stored in a MIAME supportive MySQL database (red) and reporter info is updated using the NCBI, Ensembl and UCSC genome database. Data and results are presented to the user through a web browser via the PHP scripting language. Data-normalization and other analysis or result visualization methods can be integrated using the plug-in architecture. Further data processing using the R statistical scripting language will be implemented in the near future. Results can be exported to a Progenetix or MIAME compatible format, or visualized on the genome using the Ensemble or UCSC genome browser.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC1173083&req=5

Figure 1: arrayCGHbase scheme. The data is stored in a MIAME supportive MySQL database (red) and reporter info is updated using the NCBI, Ensembl and UCSC genome database. Data and results are presented to the user through a web browser via the PHP scripting language. Data-normalization and other analysis or result visualization methods can be integrated using the plug-in architecture. Further data processing using the R statistical scripting language will be implemented in the near future. Results can be exported to a Progenetix or MIAME compatible format, or visualized on the genome using the Ensemble or UCSC genome browser.
Mentions: arrayCGHbase runs in Windows, Linux, Macintosh, and Unix environments. Particular attention was paid to the use of open source software for the development of arrayCGHbase. The software was developed in the PHP scripting language, with all data being stored in a relational, MIAME [8] (Minimal Information About a Microarray Experiment) supportive, MySQL database and communicated to the user through an Apache Web server (Figure 1). After installation on a private server, experiments can be shared by different users over the internet or a local intranet. ArrayCGHbase integrates DNA sample information, lab protocols, extracted data, and contains a plug-in architecture for data transformation, analysis, and graphical display, allowing users to develop their own modules. Reporters can be directly linked to the Ensembl [9] or UCSC [10] genome browsers, providing additional up-to-date information on each reporter. Reporters can also be manually imported into the MySQL database with the ability to update all linked experiments. The structure of arrayCGHbase was designed to follow the laboratory workflow and is compatible with all types of arrayCGH experiments and data formats (dual colour genomic clone, cDNA [11], or oligonucleotide [12] arrays spotted on any substrate, physical layout, type of array, as well as single channel hybridizations such as the Affymetrix SNP chips [13]). With a personal account and administrated access levels, a user can enter new DNA samples, annotate these, and append all relevant sample information such as quantity, quality, and applied lab protocols at each step. Each user can group experiments together into projects and, in a uniform and streamlined fashion, apply filters and transformations and run analyses. Data is exportable in several formats for offline analysis using other (dedicated) software tools, for publication or for sharing data with the research community. For advanced users, an SQL query window allows interrogation of the underlying MySQL database.

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