Abstract: The present invention provides improved systems, methods and software for determining a pathway activation strength in old subjects relative to young subjects of the same species, the method including collecting young subject transcriptome data and old subject transcriptome data for one species to evaluate pathway activation strength (PAS) and down-regulation strength for a plurality of biological pathways, mapping the plurality of biological pathways for the activation strength and down-regulation strength from old subject samples relative to young subject samples to form a pathway cloud map and providing a gero-protective rating for each of a plurality of drugs in accordance with a drug rating for minimizing signaling pathway cloud disturbance (SPCD) in the pathway cloud map of the one species to provide a ranking of the gero-protective drugs.

Abstract: The present invention provides systems, methods and software for improving robustness of transcriptomic data analysis, the method including receiving control cell transcriptomic data (C) and cell transcriptomic data (S) under study for a gene, calculating a fold change ratio (fc) for the gene, repeating these steps for a plurality of genes, grouping co-expressed genes into modules, estimating gene importance factors based on a network topology, mapped from a plurality of the modules and obtaining a insilico Pathway Activation Network Decomposition Analysis (iPANDA) value, wherein the iPANDA value has a Pearson coefficient greater than a Pearson coefficient associated with another platform for manipulating the same data.

Abstract: The present invention provides systems, methods and software for analysis of the intracellular signaling pathway activation (SPA), the method including analyzing activator and repressor roles of a plurality of gene expression gene products in a plurality of pathways in a sample of a subject to determine a pathway activation strength (PAS) for each of the plurality of pathways and comparing the pathway activation strength (PAS) in at least one sick subject with at least one healthy subject to determine intracellular signaling pathway activation (SPA) associated with a disease or disorder in the at least one sick subject.

Abstract: The present invention provides systems, methods and software for analysis of the intracellular signaling pathway activation (SPA), the method including analyzing activator and repressor roles of a plurality of gene products in a plurality of pathways in a sample of a subject to determine a pathway activation strength (PAS) for each of the plurality of pathways and comparing the pathway activation strength (PAS) in at least one sick subject with at least one healthy subject to determine intracellular signaling pathway activation (SPA) associated with a disease or disorder in the at least one sick subject.

Abstract: The present invention provides systems, methods and software for predicting drug efficacy for treating a disorder in a patient, the method including providing a drug scoring database based on pathway activation strengths (PASs) for a plurality of biological pathways associated with the drug in the treatment of the disorder, thereafter providing a support vector machines (SVM) to enable SVM tuning using a floating window to transfer data from a training dataset (T) to a validation dataset (V) by interpolation along at least one PAS axis and further determining if both i) there is a positive correlation coefficient between a drug score and a clinical efficacy of the drug and ii) an area-under a curve (AUC) statistical indicator for the drug score exceeds 0.7; to provide a predictive indication if the patient is a responder or non-responder to the drug to determine whether the drug should be used in treating the patient.

Abstract: The present invention provides improved systems, methods and software for determining a pathway activation strength in old subjects relative to young subjects of the same species, the method including collecting young subject transcriptome data and old subject transcriptome data for one species to evaluate pathway activation strength (PAS) and down-regulation strength for a plurality of biological pathways, mapping the plurality of biological pathways for the activation strength and down-regulation strength from old subject samples relative to young subject samples to form a pathway cloud map and providing a gero-protective rating for each of a plurality of drugs in accordance with a drug rating for minimizing signaling pathway cloud disturbance (SPCD) in the pathway cloud map of the one species to provide a ranking of the gero-protective drugs.

Abstract: The present invention provides systems, methods and software predicting a clinical outcome of a patient having breast cancer, the method including the steps of providing a drug score database (DSD) based on pathway activation strengths (PASs) for a plurality of biological pathways associated with the drug in the treatment of the disorder and comparing the pathway activation strengths of the plurality of biological pathways of the patient with the drug score database to provide a predictive indication if the patient is a responder or non-responder to the drug; and repeating these steps for a plurality of drugs thereby predicting a clinical outcome to the plurality of drugs of the patient to the breast cancer.

Abstract: The present invention provides systems, methods and software predicting a clinical outcome of a patient having a disorder the method including the steps of providing a drug score database (DSD) based on pathway activation strengths (PASs) for a plurality of biological pathways associated with the drug in the treatment of the disorder and comparing the pathway activation strengths of the plurality of biological pathways of the patient with the drug score database to provide a predictive indication if the patient is a responder or non-responder to the drug; and repeating these steps for a plurality of drugs thereby predicting a clinical outcome to the plurality of drugs of the patient to the disorder.

Abstract: The present invention provides systems, methods and software predicting drug efficacy for treating a disorder in a patient, the method including providing a drug score database (DSD) based on pathway manifestation strengths (PMSs) for a plurality of biological pathways associated with the drug in the treatment of the disorder and comparing the pathway manifestation strengths of the plurality of biological pathways of the patient with the drug score database to provide a predictive indication if the patient is a responder or non-responder to the drug to determine whether the drug should be used in treating the patient.