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Category Genomics>Gene Expression Analysis/Profiling/Tools Abstract ArrayGenius, Biomind's flagship product, is an enterprise software system for microarray data analysis. ArrayGenius combines advanced machine learning algorithms with massive volumes of background information, including biological ontologies, to deliver straightforward but advanced analysis.
programming in its commercial analysis software, ArrayGenius™. Most microarray analysis software packages all do the same tasks, they find the most differentiated genes between two categories, make cluster dendrograms, etc. Some of them even allow you to use knowledge resources like the Gene Ontology to drill down deeper into the biological meaning of your analytical results. All this is valuable -- but ArrayGenius is different! When microarray data is loaded into ArrayGenius, the first thing it does is compare your data to its internal ontologies -- built based on the Gene Ontology (GO) and proteomic databases -- and create an enhanced dataset. The enhanced dataset tells you the degree to which various biological processes and protein families are expressed in your dataset. ArrayGenius uses the enhanced dataset along with the original one, in all its subsequent analyses. You can make cluster dendrograms -- both the familiar kind where you see which genes cluster together in the dataset, and a new kind, where you get to observe which biological processes cluster together in the dataset. And then things get really interesting... A common situation is where microarray data samples can be divided into two or more categories. These categories may be Case vs. Control; they may represent different time points, etc. In this sort of situation, you can ask ArrayGenius to learn classification models -- mathematical rules that predict whether a sample belongs to one category or another, using the gene expression values in the sample and also the inferred expression values of biological processes and protein families in the sample. In many cases it finds extremely accurate rules -- our studies show that, after a bit of experimentation with parameter values, it generally beats the best algorithms from the academic literature. Sometimes these rules are surprisingly simple, other times they're more complex. Generally ArrayGenius will learn a lot of classification models for a dataset, Not just one or two -- and it can then study which genes, processes and families occur most often across all its models. This is a novel way of detecting which genes, processes or families are most important to the biological phenomenon being studied in the dataset. The most important features, in this sense, will often Not be the ones most differentiated in expression between the categories of interest. That's because ArrayGenius is figuring out which genes, processes and families are most important, Not in terms of their solitary activity, but in terms of their interactions with other genes, processes and families. And once you've gotten your results, you can interpret them via following hyperlinks into the Gene Ontology (GO) database, into PubMed, into various other online resources -- and into the BiomindDB, Biominds' own integrative data resource that provides useful functions like finding the research articles that focus on particular combinations of genes and processes. ArrayGenius's novel approach provides a lot of information that more traditional microarray analysis doesn't: 1) Ontological data integrated into the analytical process, so that classification rules and clusters involve biological processes and structures and families, Not just raw gene expression values. 2) A sophisticated understanding of which biological processes are important to the phenomena under analysis. 3) Extremely accurate classification rules, useful for diagnostics and other purposes. New kinds of knowledge, indicating biological relationships and research directions that would otherwise go unnoticed. A smarter way to analyze microarray data. Applications -- 1) Biomarker Discovery, including cases where biomarkers involve complex multiple gene interactions. 2) Biological Processes Interpretation, including dynamics and pathways underlying diseases and other phenotypic characteristics. 3) Personalized Medicine, including identification of individuals likely to suffer toxic reactions to particular drugs. 4) Fundamental Research, including gene function and metabolic pathway research. Product Highlights -- 1) Classification Accuracy which is industry-best (general clinical, and clinical toxicological, and general/non-clinical). 2) Powerful Reporting which condenses and summarizes results from complex analysis, including clustering and classification. 3) Most Important Features extraction from experimental data, including genes, gene products and biological processes. 4) Classification Rule Learning for predicting biological or clinical subject classification based on genetic and clinical profile data. 5) Utilization Clusters of genes or gene products which tend to be found together in the context of biological phenomenon under study. The ‘most important features’ reporting function, which highlights individual features common among hundreds or thousands of supervised classification models (classification model ensembles), is unique to ArrayGenius, and provides deeper insight when compared with rudimentary analytical methods such as tabulation or clustering of most highly expressed genes. ArrayGenius OnDemand is available for live use by subscription. ArrayGenius is also available as an enterprise application installed on qualifying Linux platforms Note: GeneGenius (another advanced Biomind product) applies an ArrayGenius-type methodology to single nucleotide polymorphism (SNP) analysis, providing immeasurable value in the case of complex diseases where No individual SNP provides much information, yet combinations of SNP's do effectively characterize conditions of interest (such as diseases). System Requirements Contact manufacturer Manufacturer Home office; see web site for international locations.
1405 Bernerd Place, Rockville MD 20851 USA Tel: (240) 505-6518 or e-mail sales@biomind.com Manufacturer's Web Site www.biomind.com/arraygenius.htm Price Contact manufacturer G6G Product Number 20145 G6G Manufacturer Number 100427 |
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