Bar Harbor Biotechnology, Inc. has developed The PerfectCircle™. A suite of products consisting of GeneSieve™ Bioinformatics, StellARrays™ Real-Time PCR Arrays, and Global Pattern Recognition™ Bioanalysis Algorithms. The PerfectCircle™ suite of products allows you to:

• Save money that would be required to develop bioinformatics and bioanalysis applications.
• Complete more experiments with your existing Real-Time PCR system.
• Incorporate your existing SYBR® Green I reagents and protocols.
• Increase sensitivity of significant fold change detection with innovative statistical analysis.
• Select any number of Real-Time PCR arrays necessary to complete your research.
• Save time that would be necessary to research and select genes and validate primer pairs.

As previously stated, the biological context of the microarray data can be defined using computational tools. These definitions provide an opportunity to both validate a hit list and simultaneously provide a means to extract additional information from that hit list.

GeneSieve™ Selects StellARrays™
With a user-friendly interface the GeneSieve™ Bioinformatics software will direct you to the most suitable StellARray™ Gene Expression / CNV System based on a series of filters and proprietary algorithms. A query using GeneSieve™ will produce a ranked list of StellARray™ Gene Expression / CNV System whose gene content has the highest likelihood of being informative for your specified biological context. Since GeneSieve™ is directly linked to our website the researcher can immediately purchase StellARray™ Gene Expression / CNV System plates (96- or 384-well) specific to your defined biological context. Then run one sample per plate on your existing Real-Time PCR system with a recommended minimum of three samples per group (a 3 vs. 3 experiment). For additional statistical power you may choose to run a 4 vs. 4 experiment: asymmetric experiments are also acceptable (e.g. 3 vs. 4, 3 vs. 5, 4 vs. 4 etc.).

StellARray™ Data is Uploaded to Global Pattern Recognition™
The real-time data is uploaded into our proprietary Global Pattern Recognition™ (GPR) software via the internet. The resulting ranked hit list is delivered to you in standard file formats (i.e. Html or Excel). The StellARrays™ are coded such that the analysis is specific to the plate content. The user inputs the kit code and the analysis is based on the proprietary Bar Harbor BioTechnology, Inc. plate map. The Global Pattern Recognition™ algorithm generates a ranked hit list of statistically significant changes between the test groups without reliance on the magnitude of the fold-change (see Akilesh S, Shaffer DJ, Roopenian D: Customized molecular phenotyping by quantitative gene expression and pattern recognition analysis. Genome Res 2003, 13:1719-1727). In addition, this algorithm eliminates the challenges associated with the definition of a 'normalizer' gene or gene set. A normalizer (or housekeeping gene) is defined as a gene whose expression level is invariant across the biological samples being analyzed. The normalization process corrects for variances in the initial sample input quantity. This assumption (an a priori definition of a single or specific set of genes as being invariant) has been shown to be fundamentally flawed and can produce data sets that are completely arbitrary (for a review see: S A Bustin, Journal of Molecular Endocrinology (2000) 25, 169-193). The use of GPR enables the experimental data to define the invariant normalizer genes, not the experimenter. Only after the genes are ranked is the magnitude of the change calculated. The magnitude is not the factor determining the rank. The use of any gene as a potential normalizer maximizes the use of the limited 'real-estate' on a plate. Each plate contains genes of potential value in defining the biological context without loss of wells used to contain potentially erroneously predefined normalizers.

Global Pattern Recognition™ Results Can Lead to GeneSieve™ analysis.
The Global Pattern Recognition™ hit list can be analyzed once again in the GeneSieve™ system and a revised biological context is defined. The revised context may redirect the user to a new StellARray™ System and the process continues until the context stabilizes thus redefining or validating the microarray signature.

De Novo Expression Analysis
Entrance into GeneSieve™ Bioinformatics without prior microarray data is also accomplished successfully. If the researcher has a field of interest based on prior work or knowledge, the GeneSieve™ process can identify the specific StellARrays™ that are highly likely to be informative for that field of study. The overall process remains the same:
1. Define the biological context in GeneSieve™ Bioinformatics
2. Access the product offerings in the Bar Harbor BioTechnology, Inc. website
3. Purchase the specified StellARray™ plate at Lonza
4. Collect the data
5. Upload to the data to the Global Pattern Recognition™ software
6. Download the results

Continue the process until your biological context stabilizes and your results either support your experiment or redefine the entire biological pathway. At this time depart The PerfectCircle™ with the results necessary to draw a conclusion regarding your gene research experiment.

Read more about:
GeneSieve™
StellARrays™
Global Pattern Recognition™