Abstract: A method for evaluating hepatocellular carcinoma in a subject is provided. In certain embodiments, the method comprises: a) obtaining a hepatocellular carcinoma protein marker profile for a sample obtained from the subject; and b) comparing the protein marker profile to a control profile.

Abstract: A method for evaluating hepatocellular carcinoma in a subject is provided. In certain embodiments, the method comprises: a) obtaining a hepatocellular carcinoma protein marker profile for a sample obtained from the subject; and b) comparing the protein marker profile to a control profile.

Abstract: Embodiments of the present invention include methods and systems for analysis of comparative genomic hybridization (“CGH”) data, including CGH data obtained from microarray experiments.

Abstract: Various embodiments of the present invention determine various quality metrics that reflect the quality of two or more identically-executed or similar array-based comparative-genomic-hybridization (“aCGH”) experiments. In certain embodiments of the present invention, a pairwise quality metric is generated for each possible pair of aCGH experimental results within a set of aCGH experimental results. The pairwise quality metrics may be summed and optionally normalized to produce an overall quality metric for the set of aCGH experimental results. Various pairwise quality metrics can be used in different embodiments of the present invention, including pairwise quality metrics based on measures of aberration overlap.

Abstract: Embodiments of the present invention include methods and systems for analysis of comparative genomic hybridization (“CGH”) data, including CGH data obtained from microarray experiments.

Abstract: The invention provides genes (DEA genes) that are differentially expressed in atherosclerotic lesions and polypeptides encoded by these genes. The invention provides compositions comprising a targeting agent conjugated to a functional moiety, wherein the targeting agent selectively binds to a polypeptide encoded by one a DEA gene. The functional moiety can be an imaging agent, therapeutic agent, etc. The invention further provides methods for providing diagnostic or prognostic information related to atherosclerosis involving detecting expression or activity of an expression product of one or more of the DEA genes. The invention further provides therapeutic methods comprising administering to a subject a composition comprising a targeting agent conjugated to a functional moiety that binds selectively binds to a polypeptide encoded by a DEA gene.

Abstract: Various embodiments of the present invention are directed to methods and systems for automatic, statistically meaningful detection of aberrations common to multiple samples within a sample set. Many various aberration-calling techniques are used to identify aberrant intervals within each of the samples of the sample set. A set of candidate intervals is constructed to include the aberrant intervals identified by the aberration-calling technique, as well as two-way intersections of the identified aberrant intervals. A score indicating the statistical relevance of each candidate interval with respect to each sample is next assigned to each candidate interval. Then, a total significance score is assigned to each candidate interval based on the individual scores for the candidate interval with respect to each sample. The most statistically significant candidate intervals may be selected based on the total significance scores assigned to the candidate intervals.

Abstract: Methods and compositions for performing sample heterogeneity corrected comparative genomic hybridization (CGH) are provided. In the subject methods, an initial CGH result is processed to account for potential sample heterogeneity to obtain a sample-heterogeneity corrected CGH result. Also provided are methods for evaluating candidate surface-bound nucleic acids, e.g., candidate aCGH probe nucleic acids, to identify probes useful in assaying heterogeneous samples.

Abstract: In various embodiments of the present invention, initial gene-expression data is initially partitioned into classes by patient, subject, or other identifier of a source of samples, expression-level-differences are computed for each gene with respect to each initial partition, and a rank consistency score or fold-change consistency score is computed for each gene from the expression-level difference metrics computed for each initial partition. In other words, rather than partitioning gene-expression-level data directly into two or more classes relative to an event of interest, the gene-expression-level data is first partitioned according to sample source, and then each sample-source partition is partitioned into two or more classes relative to an event of interest. Levels of significance, or p-values, can be straightforwardly computed for both rank consistency scores and fold-change consistency scores.

Abstract: Methods, tools, systems and computer readable media for analyzing CGH data, together with data from an independent source. Independent data is compared with the CGH data, wherein the CGH data is characterized by sets of defined regions differentiated by at least one property. Enrichment is assessed for at least one subset of the data from an independent source with regard to at least one of the sets of defined regions in the CGH data. Methods, tools, systems and computer readable media for visualizing CGH data as it is impacted by data from an independent source are also provided. A relationship between at least one defined set of the CGH data and at least one set of sequence elements defined in the data from an independent source may be visualized.

Abstract: Various embodiments of the present invention are directed to a system and methods for minimizing risk factors that contribute to the development of vascular graft disease and vascular graft failure. In one embodiment, a microarray-based gene expression analysis may be employed to select pre-implanted vessel candidates suitable as grafts in various vascular transplantation procedures. By using a microarray that includes a set of probe sequences that statistically correlate with vascular graft disease, mRNA expression levels of vascular-graft-disease-related genes within vessel-graft candidates can be determined to produce an expression profile for each vessel tested. Such molecular profile of genes related to various forms of vascular graft disease enables clinicians to select a vessel graft having the lowest probability of developing vascular graft diseases, and having the highest probability of maintaining adequate patency rate.

Abstract: In various embodiments of the present invention, initial experimental data is initially partitioned into classes by sample source, concentration or number-of-molecule values are computed with respect to each initial partition, and a rank consistency score or fold-change consistency score is computed for various molecular concentration or number-of-copies determinants with respect to one or more class-specifying events of interest. In other words, rather than partitioning experimental data directly into two or more classes relative to an event of interest, the experimental data is first partitioned according to sample source, and then each sample-source partition is partitioned into two or more classes relative to an event of interest.

Abstract: The present invention provides polynucleotides and polypeptides (VECSM polynucleotides and polypeptides) that are differentially expressed in vascular endothelial cells. The invention further provides a variety of compositions, diagnostic, and therapeutic methods based on identification of these markers. In particular, the invention provides a targeting agent linked to a functional moiety, wherein the functional moiety can comprise any of a number of different agents, including imaging agents, cytotoxic agents, and stimulators or inhibitors of angiogenesis.

Abstract: The invention identifies genes whose expression is upregulated or downregulated following mechanical offloading in subjects with heart failure. The invention provides compositions comprising a targeting agent conjugated to a functional moiety, wherein the targeting agent selectively binds to a polypeptide encoded by one of these genes. The functional moiety can be an imaging agent, therapeutic agent, etc. The invention further provides methods for providing diagnostic or prognostic information related to heart failure involving detecting expression or activity of an expression product of one or more of the identified genes. The invention further provides diagnostic and therapeutic methods comprising detecting or administering an apelin peptide to a subject.

Abstract: The present invention provides systems and methods for determining the cell type composition of a mixed cell population. The invention provides systems and methods for identifying and defining pure cell type specific signatures. These pure cell type specific signatures may be used to determine the cell type composition of a mixed cell population. The systems and methods of the invention may be used for a variety of research and clinical purposes. For example, they may be used to detect the presence or absence of cells of particular types, and to determine whether variations in gene expression, e.g., between different samples, represent true changes in gene expression or differences in cell type composition of the samples.

Abstract: Methods and reagents are disclosed for quantitatively analyzing a set of target nucleic acid sequences. In the method a unique set of oligonucleotide probe precursors is hybridized to the target nucleic acid sequences to produce hybrids. The hybrids are processed to alter the mass of each of the oligonucleotide probe precursors in the hybrids in a target sequence-mediated reaction to produce oligonucleotide products, each of which has a unique mass that is not a result of the presence of a mass tag in the oligonucleotide product. The processing of the hybrids may involve polymerase extension or ligation. The products are analyzed by means of mass spectrometry and the results are related to the amount of the target nucleic acid sequences in the set. Kits for carrying out the above methods are also disclosed.