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Main Features of BxAF EzArray |
- No pre-knowledge of microarray data analysis is required.
- Get analysis results in minutes.
- Customize analysis procedures in your ways.
- Download all analysis intermediate/final files and run analysis again locally.
- Though no programming is necessary, you can still provide your own scripts for data analysis.
- Powered by BxAF technologies for high security, integrated data management, data sharing among team members.
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BxAF EzArray Process Flowchart |
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EzArray system architecture |
| EzArray is a multi-user system with web interfaces. All users must first register, and their accounts will become active upon approval by system administrators. User login information is stored in MySQL database with encryption, making EzArray a highly secure system. |
Microarray data management and sharing in EzArray |
In EzArray, data are either stored in MySQL database or on the server as files. Microarray data are organized by projects, and a user can create unlimited projects. In each project, only one array chip type is allowed. Besides Affymetrix chip type names such as hug133plus2, users can also enter Gene Expression Omnibus (GEO) platform names such as GPL570. The array sample information and the CEL files generated from Affymetrix GeneChip Operating System can be added one-by-one or imported into a project in batch. In EzArray data analysis can be performed with all samples in a project or just a few selected samples.
EzArray projects, samples, and analysis results entered by a user may be shared with group members in read-only mode. However, EzArray administrators can adjust data sharing methods by changing the settings in the configuration file. |
Microarray data analysis procedures in EzArray |
Microarray data analysis in EzArray is highly automated such that even novice users can perform initial analysis and get results instantly. Experienced users can also use the system with full control of the analysis procedures. In general, microarray data analysis is performed step-by-step with these programs:
- PreQ – preprocessing, normalization, and quality control plots;
- ProS – statistical procedures for detecting differentially expressed genes; and
- RepA – gene annotation and linking to public databases
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Re-analysis of previously published microarray data |
EzArray contains tools to retrieve the descriptive information of all GEO records, including Platforms, Series, Samples, and DataSets. EzArray also contains a simple search form allowing users to search for DataSets (Figure 3A). The search results include a list of DataSets with links to GEO website. Users can select one or more DataSets from the list and create projects for data re-analysis. EzArray downloads the corresponding DataSet files automatically from the GEO website.
Analysis of GEO microarray data may be started from raw microarray data (e.g. .CEL files) or pre-processed expression value data originally submitted by previous authors. In the first case, if authors have submitted .CEL files to GEO, EzArray will automatically download these supplementary files and link them to the newly created projects. Then users can perform data analysis with EzArray programs as previously stated. In the second case, regardless of whether authors submitted raw microarray data or not, EzArray retrieves curated datasets from GEO, extracts the dataset information, and stores them in the project, which can be readily used to perform data re-analysis with program ProS directly without performing data pre-processing with PreQ. |
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