Acuity 4.0

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract Acuity 4.0 is an advanced enterprise microarray informatics platform for microarray data storage, data filtering and data analysis.

Acuity Analysis features include:

Normalization - Acuity's Normalization Wizard can be used to normalize an arbitrary number of microarrays. You can normalize on all spots, control spots, negative controls or any other subset of spots that you can specify with a fully general database query. Normalize groups of microarrays to a time point or a sample. Choose linear ratio-based methods or non-linear lowess methods, including print-tip groups. Once you are finished, unnormalized and normalized data can be displayed side-by-side in the Normalization Viewer.

Filtering - Product offers a large number of analytical and statistical tools that you can use to filter out noise from your data: filter on replicate statistics, on individual spot characteristics or on many other quality measures.

Replicate Analysis - Replicate substances are automatically combined, and can be filtered by standard deviation, coefficient of variation and many other measures. Replicate microarrays can be combined to construct representative data points from each time or for each tissue in an experiment.

Find Matching Expression - You can use Acuity's Match Expression function to investigate the behavior of individual substances in your experiment. It offers nine (9) different similarity metrics to find the substances that are most highly correlated with a single profile or to an average profile built from a class of substances.

Many Clustering Methods - Acuity offers a suite of advanced analysis methods, among them Hierarchical Clustering, Self-Organizing Maps, K-Means and K-Medians, Gap Statistic, Principal Components Analysis, Gene Shaving and more. Each algorithm offers a large choice of similarity metrics, so that you can use the analysis that is appropriate for your data. You can use the output of one algorithm as input to the next. For example, you can optimally order the branches in a dendrogram from a hierarchical cluster, with the order derived from a Self-Organizing Map or a Principal Components Analysis.

Performance Optimization - All Acuity analyses have been optimized for speed and memory use on very large data sets so that a standard desktop computer can be used to cluster hundreds of microarrays. Clustering and other processor-intensive tasks are implemented as background processes, so that you can queue and execute multiple analysis tasks while continuing to work on other tasks in Acuity.

Analysis Audit Trail - All Acuity analysis operations and results are stored sequentially in the database as they are calculated, so an audit trail is maintained automatically and displayed in the Acuity project tree for each data set.

Substance and Microarray Lists (Quicklists) - Acuity Quicklists are an advanced method of saving lists of interesting substances, microarrays or annotations. Each list can be assigned a color. Together with the ability to apply a list to the current view of the data, so that the substances and microarrays are colored appropriately, colored quicklists give you the ability to track multiple sets of substances through all Acuity visualizations.

Reports and Scripting - Acuity supports standard scripting languages such as VBScript and JavaScript, as well as any other scripting languages supported by Internet Explorer, such as PerlScript and PythonScript.

Acuity Visualizations features include:

Clear and Interactive - Acuity displays clustering results in many different ways, uses smooth interactive 3-D plots of principal components data (exportable as AVI animations), and synchronizes all views so that substances and their annotations selected in one view are automatically grouped in all other views. Color Tables - The Color Table is the central data view in Acuity. Microarrays are organized into columns, with substances in rows. The table is colored automatically based on user-specified thresholds, and these colors are propagated throughout Acuity.

Additional Visualizations features include - Expression Profiles; 3D Scatter Plots; Microarray and Substance Summaries; Single Microarray View; Web Links; Pathway Links; and the ability to save analysis visualizations as a Portable Document Format (PDF) file. Acuity Data Management features include - A Scaleable Relational Database; Ability to Manage Multiple Users; Full Integration with GenePix Pro; The Acuity Project Tree; Full Database Queries via The Query Wizard; Export microarray info in MAGE-ML format; Fully Track Microarray data; Acuity database can manage annotations automatically; Universal Text File Import; Advanced Database Management Tools; and more.

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Manufacturer Web Site Molecular Devices Corporation

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G6G Abstract Number 20009

G6G Manufacturer Number 101822