Abstract: The invention described herein relates in part to compositions, biomarkers and methods for diagnosis and prognosis of prostate lesions, including prostate cancer, including a tissue-based assay providing diagnostic and prognostic information related to prostate cancer. In some embodiments, the invention further relates to improvements in the ability to accurately diagnose prostate cancer, detect early-stage prostate cancer, and localize prostate lesions within the three-dimensional space of the prostate.

Abstract: Described are embodiments related to prostate cancer biomarkers, agents, and systems for detecting and targeting the same, and associated prostate cancer diagnostic and prognostic methods.

Abstract: Among the methods, compositions, combinations and kits provided herein are those for determining gene expression levels in one or more cell types in heterogeneous cell samples, for identifying genes differentially expressed in different cell types, and for detecting a cell type in a sample from a subject. Also provided herein are methods, compositions, combinations and kits for determining gene expression levels in cells corresponding to phenotypes, and for identifying a phenotype of a subject by detecting differentially expressed genes.

Abstract: Materials and Methods related to diagnosing and/or determining prognosis of prostate cancer.

Abstract: Among the methods, compositions, combinations and kits provided herein are those for determining gene expression levels in one or more cell types in heterogeneous cell samples, for identifying genes differentially expressed in different cell types, and for detecting a cell type in a sample from a subject. Also provided herein are methods, compositions, combinations and kits for determining gene expression levels in cells corresponding to phenotypes, and for identifying a phenotype of a subject by detecting differentially expressed genes.

Abstract: The present invention provides methods and compositions for isolating a nucleic acid molecule fragment comprising at least a portion of a gene, comprising: stimulating at least one cell or at least one nucleus with radiation; cross-linking at least one transcription factor to a nucleic acid molecule in said at least one cell or at least one nucleus with formaldehyde, forming at least one transcription factor-nucleic acid molecule complex; fragmenting said nucleic acid molecule to form at least one transcription factor-nucleic acid molecule fragment complex; and isolating the nucleic acid molecule fragment from said at least one transcription factor-nucleic acid molecule fragment complex to form at least one isolated nucleic acid molecule fragment; wherein said at least one isolated nucleic acid molecule fragment comprises at least a portion of the first exon of a gene whose expression is modulated by said transcription factor; further wherein said at least one isolated nucleic acid molecule fragment comprises

Abstract: Oligonuclotides, compositions and methods for modulating the over-expression of EGR-1 in cancer cells. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding Egr-1. Methods include using these compounds for modulation of Egr-1 expression in cancer cells in which Egr-1 is over-expressed for the treatment of cancer.

Abstract: The present invention provides compositions that can be administered to an individual and inhibit a stress activated protein kinase pathway. The invention also provides methods of increasing the sensitivity of cancer cells to a cancer therapy by contacting the cancer cells with a stress activated protein kinase pathway inhibitor. The invention further provides methods of reducing the severity of a cancer in a patient by administering to the patient a stress activated protein kinase pathway inhibitor and treating the patient with a conventional cancer therapy.

Abstract: The present invention provides compositions that can be administered to an individual and inhibit a stress activated protein kinase pathway. The invention also provides methods of increasing the sensitivity of cancer cells to a cancer therapy by contacting the cancer cells with a stress activated protein kinase pathway inhibitor. The invention further provides methods of reducing the severity of cancer in a patient by administering to the patients a stress activated protein kinase pathway inhibitor and treating the patient with a conventional cancer therapy.

Abstract: The present invention provides compositions that can be administered to an individual and inhibit a stress activated protein kinase pathway. The invention also provides methods of increasing the sensitivity of cancer cells to a cancer therapy by contacting the cancer cells with a stress activated protein kinase pathway inhibitor. The invention further provides methods of reducing the severity of a cancer in a patient by administering to the patient a stress activated protein kinase pathway inhibitor and treating the patient with a conventional cancer therapy.

Abstract: The present invention provides methods for the identification of nucleic acid molecules corresponding to genes regulated by a transcription factor comprising: cross-linking a transcription factor to a nucleic acid molecule in a cell forming a transcription factor-nucleic acid molecule complex; fragmenting the nucleic acid molecule to form a transcription factor-nucleic acid molecule fragment complex; isolating the nucleic acid molecule fragment; combining the isolated nucleic acid molecule fragment with a cDNA library of sequences known to be complementary to previously identified nucleic acid molecules, or a cDNA obtained by reverse transcription of a population of RNA molecules, to form a mixture comprising an isolated nucleic acid molecule fragment-cDNA complex; amplifying the cDNA in the isolated nucleic acid fragment-cDNA complex using the nucleic acid molecule fragment as a primer; and identifying the amplified cDNA molecule by sequencing the cDNA molecule and comparing to known sequences or hybridizati

Abstract: One aspect of the present invention is a method for isolating at least one nucleic acid molecule comprising at least a portion of a gene, including: cross-linking at least one transcription factor to a nucleic acid molecule in at least one cell or at least one nucleus, forming at least one transcription factor/nucleic acid molecule complex; fragmenting the nucleic acid molecule to form at least one transcription factor/nucleic acid molecule fragment; and isolating at least one nucleic acid molecule from said at least one transcription factor/nucleic acid molecule fragment to form at least one isolated nucleic acid molecule fragment; wherein said at least one isolated nucleic acid molecule fragment comprises at least a portion of the first exon of a gene whose expression is modulated by said transcription factor; further wherein said at least one isolated nucleic acid molecule fragment comprises at least one transcription factor binding site that is in close proximity to or operably linked to said first exon o