OncoFinder Platform is an oncology solution to analyze the gene expression data from microarray datasets by measuring the activation of intracellular signaling pathways. It allows you to compare data obtained using multiple platforms and minimize the errors introduced by high-throughput sequencing. This makes it possible to analyze the features of intracellular regulation on a mathematical basis and perform data analysis independently of different microarray types. The ability of OncoFinder to characterize the functional states of transcriptomes and interactomes more accurately than before makes it a method of choice for genetics, physiology, biomedicine, molecular diagnostics, and many other applications.
OncoFinder maps the gene expression data onto known and custom intracellular signaling pathways. These pathways regulate numerous processes involved in normal and pathological conditions including development, growth, aging, and cancer. Analysis of these signaling pathways makes it possible to measure differences in physiological state such as aging, disease, or chemical exposure among individual samples using microarray data. The difference in gene expression among signaling pathways can be used to predict which drugs and other interventions will be most effective for improving health. For example, OncoFinder can be used by clinicians to analyze the effectiveness of drugs for cancer treatment or used by researchers to determine pathways involved in age-related diseases.
OncoFinder is distinguished by its unique algorithm that quantifies perturbations for each signaling pathway. This makes it possible to quantitatively estimate the extent of each signaling pathway activation in a given sample relative to the control sample or a set of control samples. The algorithm separates the positive/activator and negative/repressor role of each gene in the pathway to determine the role of each gene in signal transduction and calculate the pathway activation strength. The pathway activation strength measures the degree of functional changes in the regulation of a signaling pathway, with positive or negative values indicating if the pathway is up-
or down-regulated, respectively. Using the pathway activation strength, OncoFinder scores drugs based on their involvement in each signaling pathway and the ability of the drug to restore healthy gene expression.
OncoFinder currently features more than 700 pathways in the Biochem Database, with pathways for intracellular cell signaling and metabolism in humans. It also features mouse signaling pathways. The database contains over 150 drugs.
To learn more about how OncoFinder works, please read the following papers:
OncoFinder's biomathematical method can be used for both quantitative and qualitative analysis of intracellular signaling pathway activation (SPA). This method is universal and may be used for the analysis of any physiological, stress, malignancy, or other perturbed condition at the molecular level. In contrast to other existing techniques for aggregation and generalization of gene expression data from individual samples, we suggest to distinguish the positive/activator and negative/repressor role of every gene product in each pathway. We show that the relative importance of each gene product in a pathway can be assessed using kinetic models for “low-level” protein interactions.
OncoFinder gives its partners a personal workspace that allows to manage projects easily. Partners may access their data anywhere by uploading it to the website, and may organize their workspace into multiple projects so that related datasets may be kept together. Once their files are uploaded, partners may perform calculation of signaling pathway activation strength at any time and download full reports in a single file. OncoFinder provides the option to create a public project that a partner may share with other users or create a private project that only the patner may see.
Due to its universal applicability, the method OncoFinder, published in the beginning of March 2014, is already widely used by the researcher community globally.
The OncoFinder platform enables researchers to calculate the Drug Score index that makes it possible to range the existing anticancer drugs according to their potential for to selectively kill the cancer cells of an individual patient. Each study performed by the OncoFinder team is personalized, since anticancer drug analysis is based strictly on the patient-specific gene expression data.