The mAdb microarray database and analysis system (11) is a core component of ERIC. This is a web-based system that supports sharing of data between groups and includes a microarray storage database and a variety of built-in analysis tools. mAdb can import Affymetrix data as well as spotted arrays, and can use the quantitation and composite image files from a number of microarray scanners. The central concept for mAdb is that of creating filtered, reusable data sets for analyzing microarray data. Once the raw data is processed and placed in ERIC's relational database, a user can filter the data for quality, using a variety of filters for spot size, signal/background ratio, excluding those spots marked as ‘Bad’ or ‘Not Found’ by the scanner software, as well as a number of other quantitative metrics. Normalization can be done either on the raw data or only on those spots which pass the spot quality criteria set by the user. This creates a parent-filtered data set, which can be further filtered in other ways, such as by expression ratios, by genes (rows) or by arrays (columns), or used directly in the analysis tools. Each data set maintains a history associated with it, so users can see how it was derived.
The analysis tools allow hierarchical, K-means and self-organizing map-based clustering of the data by a number of metrics and linkage methods, as well as other related visualization techniques such as scatter plotting, Principal Components Analysis, and Multidimensional Scaling. Graphics can be exported for publication and protocols for MIAME-formatted data can be stored.
Microarray data is linked to corresponding annotated features in ERIC genomes to provide a way to access up-to-date annotation records while viewing data in mAdb. There are security controls for access to data in mAdb. All users must register for an account. With an account, users have access to publicly available projects and their own private workspace that is only available to themselves and other users that they grant access to the project. Users can collaborate on experiments and analyses in their secure workspace, and if they desire, make data available for analysis by all users.
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