Technology - Bioinformatics Software for Systems Biology
Systems Reconstruction (SR) technology and OMICS data analysis
At GeneGo, we believe that functional analysis of inherently complex high-throughput data for systems biology must be based on a fundamental understanding of human biology. That means drawing on the unparalleled resources of our one-of-a-kind, manually curated database of experimentally proven protein-protein, protein-DNA and protein-compound interactions, and being able to perform integrated and comparative analyses of multiple data types using advanced algorithms derived from an in-depth understanding of signaling and metabolic pathways. In short, rigorous and robust cheminformatics and bioinformatics software is required. A comprehensive systems biology platform should:
- be capable of accommodating different types of experimental data
- be based on experimental data integrated from a broad foundation of small-scale experiments
- offer an easy to use toolkit and interface for data visualization and analysis
- feature bioinformatics software that is compatible with a variety of biology, chemistry and clinical databases
- include knowledge for stimuli, signaling and effect in cell life
When it came to bioinformatics software, Genego applied these criteria for systems biology to develop its patent-pending core technology platform called Systems Reconstruction™. GeneGo scientists assembled experimentally proven enzymatic reactions and signaling protein interactions into a series of interconnected networks. The complete set of interactions defines the molecular machinery of human cells and encompasses an almost infinite number of multi-step pathways and complexes. Only a fraction of the proteins represented are expressed and active at any given time, and only a small subset of possible connections is activated. This subset can be identified by superimposing the experimental OMICS datasets on the networks. Through our bioinformatics software, identification of a subset of active, interconnected proteins and genes leads to the "reconstruction" of the subsystem as a vertically organized combination of multi-step pathways, from membrane receptors via signal transduction cascades, to transcriptional factors and, finally, to core effectors, comprised of metabolic pathways and structural complexes.
To accommodate the complex aspects of mammalian functionality— such as coordinated expression of multiple genes to bring about a prescribed function, splice variants, and protein isoforms, complexes, and families — GeneGo has developed a database of novel architecture. Unlike other integration platforms in systems biology that have molecular entities (genes, proteins) as principal objects, GeneGo's SR system is pathway-centered and redefines biological "entities," "elements", "blocks" and the various types of directed connections that link them. This innovative architecture in our patented bioinformatics software allows SR to superimpose all relevant information derived from direct high throughput experiments and from the literature onto pathways and, importantly, to cross-validate different types of data.