Abstract: Provided herein are methods of determining tumoral sensitivity to hormonal (endocrine) therapy based upon an index of estrogen receptor (ER)- and progesterone receptor (PR)-related genes, referred to as the sensitivity to endocrine therapy index (SETER/PR index), and may have additional consideration for the proportion of ER gene (ESR1) RNA transcripts that contain a mutation relative to the value of the SETER/PR index. Further provided are methods of treating breast cancer patients determined to be sensitive to an endocrine therapy by the SETER/PR index.

Abstract: Provided herein are methods of determining tumoral sensitivity to hormonal (endocrine) therapy based upon an index of estrogen receptor (ER)- and progesterone receptor (PR)-related genes, referred to as the sensitivity to endocrine therapy index (SETER/PR index), and may have additional consideration for the proportion of ER gene (ESRI) RNA transcripts that contain a mutation relative to the value of the SETER/PR index. Further provided are methods of treating breast cancer patients determined to be sensitive to an endocrine therapy by the SETER/PR index.

Abstract: Provided herein are methods of determining tumoral sensitivity to hormonal (endocrine) therapy based upon an index of estrogen receptor (ER)- and progesterone receptor (PR)-related genes, referred to as the sensitivity to endocrine therapy index (SETER/PR index), and may have additional consideration for the proportion of ER gene (ESRI) RNA transcripts that contain a mutation relative to the value of the SETER/PR index. Further provided are methods of treating breast cancer patients determined to be sensitive to an endocrine therapy by the SETER/PR index.

Abstract: A method of evaluating a cancer patient comprising evaluating gene expression levels in a patient sample, calculating a predictor score using the gene expression levels, and assessing the likelihood of a therapeutic outcome using the predictor score is disclosed.

Abstract: The present invention provides the identification and combination of genes that are expressed in tumors that are responsive to a given therapeutic agent and whose combined expression can be used as an index that correlates with responsiveness to that therapeutic agent. One or more of the genes of the present invention may be used as markers (or surrogate markers) to identify tumors that are likely to be successfully treated by that agent or class of agents such as hormonal or endocrine therapy or chemotherapy.

Abstract: A method of evaluating a cancer patient comprising evaluating gene expression levels in a patient sample, calculating a predictor score using the gene expression levels, and assessing the likelihood of a therapeutic outcome using the predictor score is disclosed.

Abstract: The present invention provides the identification and combination of genes that are expressed in tumors that are responsive to a given therapeutic agent and whose combined expression can be used as an index that correlates with responsiveness to that therapeutic agent. One or more of the genes of the present invention may be used as markers (or surrogate markers) to identify tumors that are likely to be successfully treated by that agent or class of agents such as hormonal or endocrine therapy or chemotherapy.

Abstract: The present invention provides the identification of genes that are expressed in tumors to indicate responsiveness or resistance to an agent or class of agents. More particularly, these genes show expression associated with responsiveness to one agent or class of agents is inversely related to expression in association with another class of agents. One or more of theses genes of the present invention can be used as markers (or surrogate markers) to identify tumors that are likely to be successfully treated by the responsive agent as well as to identify tumors that should avoid treatment by the resistant agent.

Abstract: Disclosed is a method for determining survival and relapse of a patient undergoing therapy for a tumor by determining a residual cancer burden index based on the bidimensional diameters of a primary tumor bed of said tumor in a resection specimen, the proportion of the primary tumor bed area that contains invasive carcinoma, the number of regional lymph nodes containing metastatic carcinoma, the diameter of the largest metastasis in an regional lymph node; and the fractional reduction in lymph node size with each added positive lymph node.

Abstract: Method of Measuring Residual Cancer and Predicting Patient Survival Disclosed is a method for determining survival and relapse of a patient undergoing therapy for a tumor by determining a residual cancer burden index based on the bidimensional diameters of a primary tumor bed of said tumor in a resection specimen, the proportion of the primary tumor bed area that contains invasive carcinoma, the number of regional lymph nodes containing metastatic carcinoma, the diameter of the largest metastasis in an regional lymph node; and the fractional reduction in lymph node size with each added positive lymph node.

Abstract: The present invention provides the identification and combination of genes that are expressed in tumors that are responsive to a given therapeutic agent and whose combined expression can be used as an index that correlates with responsiveness to that therapeutic agent. One or more of the genes of the present invention may be used as markers (or surrogate markers) to identify tumors that are likely to be successfully treated by that agent or class of agents such as hormonal or endocrine treatment.

Abstract: Methods are provided for estimating the risk of developing melanoma and related malignancies in an individual. Methods and compositions for diagnosing, treating, and preventing melanoma and related malignancies also are provided.

Abstract: The invention relates to the gene encoding the mammalian E2IG3 and its product. More specifically, the invention relates to the diagnosis of aberrant E2IG3 gene or gene product expression, the identification, production, and use of compounds which modulate E2IG3 expression or the activity of the E2IG3 gene product including but not limited to nucleic acid encoding E2IG3 and homologues, analogues, and deletions thereof, as well as antisense, ribozyme, triplehelix, antibody, and polypeptide molecules as well as small inorganic molecules; and pharmaceutical formulations and routes of administration for such compounds.

Abstract: The present invention provides methods for identifying relationships between gene expression and protein modifications in a cell by determining gene expression generated in the cell, determining protein modifications generated in the cell, and coordinating the gene expression and protein modifications generated in the cell. Also provided by the present invention is a computer system for identifying such a relationship between gene expression and protein modifications. The present inventive methods and computer systems are useful for investigating a variety of physiological or pathophysiological processes, including metabolic pathways, typing of diseased cells, and identifying biological activities of test materials.

Abstract: A multi-function process is described for the hydrolysis and fractionation of lignocellulosic biomass to separate hemicellulosic sugars from other biomass components such as extractives and proteins; a portion of the solubilized lignin; cellulose; glucose derived from cellulose; and insoluble lignin from said biomass comprising one or more of the following: optionally, as function 1, introducing a dilute acid of pH 1.0-5.0 into a continual shrinking bed reactor containing a lignocellulosic biomass material at a temperature of about 94 to about 160.degree. C. for a period of about 10 to about 120 minutes at a volumetric flow rate of about 1 to about 5 reactor volumes to effect solubilization of extractives, lignin, and protein by keeping the solid to liquid ratio constant throughout the solubilization process; as function 2, introducing a dilute acid of pH 1.0-5.