Abstract: A method, apparatus, and computer program product for analyzing gene expressions is presented. An operation is performed for determining a gene expression pattern for a condition, wherein the gene expression pattern comprises a gene expression. Next, a spatial-expression pattern is formed by selecting a chromosomal region having an exon; and associating the gene expression within the gene expression pattern with its corresponding exon. A further operation may be performed, where in the forming of the spatial-expression pattern, a spatial-expression pattern signal is created as a representation of the spatial-expression pattern. The magnitude of the spatial-expression pattern signal at any point is determined by an expression level of the corresponding exon. Spatial patterns may be identified in the signal by means of various signal processing techniques such as Fourier or Wavelet transforms.

Abstract: A method, apparatus, and computer program product for analyzing gene expressions is presented. An operation is performed for determining a gene expression pattern for a condition, wherein the gene expression pattern comprises a gene expression. Next, a spatial-expression pattern is formed by selecting a chromosomal region having an exon; and associating the gene expression within the gene expression pattern with its corresponding exon. A further operation may be performed, where in the forming of the spatial-expression pattern, a spatial-expression pattern signal is created as a representation of the spatial-expression pattern. The magnitude of the spatial-expression pattern signal at any point is determined by an expression level of the corresponding exon. Spatial patterns may be identified in the signal by means of various signal processing techniques such as Fourier or Wavelet transforms.

Abstract: A method, apparatus, and computer program product for analyzing gene expressions is presented. An operation is performed for determining a gene expression pattern for a condition, wherein the gene expression pattern comprises a gene expression. Next, a spatial-expression pattern is formed by selecting a chromosomal region having an exon; and associating the gene expression within the gene expression pattern with its corresponding exon. A further operation may be performed, where in the forming of the spatial-expression pattern, a spatial-expression pattern signal is created as a representation of the spatial-expression pattern. The magnitude of the spatial-expression pattern signal at any point is determined by an expression level of the corresponding exon. Spatial patterns may be identified in the signal by means of various signal processing techniques such as Fourier or Wavelet transforms.

Abstract: The invention provides system and methods for analyzing the perturbation of one or more biological pathways. In one embodiment, expression values for each of a plurality of genes for one or more experimental conditions may be received. Gene differential regulation values may then be calculated for each of the plurality of genes across each of the one or more experimental conditions. The gene differential regulation values may then be grouped by the biological pathway and experimental condition from which each gene differential regulation value originated yielding one or more pathway-condition data sets. Pathway perturbation values may then for each of the one or more pathway-condition data sets using the gene differential regulation values. These pathway perturbation values may be clustered, used to identify biological pathways or experimental conditions for further analysis, and/or utilized to build a classifier for classifying additional experimental data.

Abstract: An apparatus, method, and computer program product are provided for determining a confidence measure for the output of a process for assessing proteomic and genomic information samples. Typically, data is received as the results from a microarryi experiment. The confidence measure is intended to determine whether the results of the experiment have been degraded due to experimental error. Several criteria are used by which quality is determined. The criteria are preferably combined into a combined quality measure in order to account for several possible sources of error.

Abstract: Described is a system for analysis and visualization of genomic data. The system allows a user to select at least one individual sample. The sample has chromosomal data representing a genome with a chromosome and also includes chromosomal measurements of at least one event at a particular location on the chromosome. A frequency of event is generated based on the selected sample. The frequency of event is a frequency of occurrence of the event in the selected sample. At least one annotation can be selected that includes chromosomal region specific information as related to the chromosome. Finally, the chromosomal data, the annotation, and the frequency of event on a display can all be simultaneously displayed, thereby allowing a user to view chromosomal region specific information with respect to a particular chromosomal event.

Abstract: An apparatus, method, and computer program product are provided for determining a confidence measure for the output of a process for assessing proteomic and genomic information samples. Typically, data is received as the results from a microarry experiment. The confidence measure is intended to determine whether the results of the experiment have been degraded due to experimental error. Several criteria are used by which quality is determined. The criteria are preferably combined into a combined quality measure in order to account for several possible sources of error.

Abstract: A digital image processing-based system and method for quantitatively processing a plurality of nucleic acid species expressed in a microarray are disclosed. The microarray is a grid of a plurality of sub-grids of the nucleic acid species. The system includes a scanner that has a digital scanning sensor that scans the microarray and transmits from an output a digital image of the microarray, and a processor that receives the digital image of the microarray from the scanner and then processes the digital image, identifying each of the microarray's sub-grids. The processor then detects in each of the sub-grids a center-representing pixel of a signal of a chemical material and an approximate radius of the signal. Then, the processor segments the signal and calculates a characterizing measure for the segmented signal.

Abstract: A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. The frame is stored in a memory device and a set of image information within said frame including a selected set of the DNA spot images is selected. A grid including a plurality of spaced grid points corresponding to said selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame.

Abstract: A digital image processing-based system and method for quantitatively processing a plurality of nucleic acid species expressed in a microarray are disclosed. The microarray is a grid of a plurality of sub-grids of the nucleic acid species. The system includes a scanner that has a digital scanning sensor that scans the microarray and transmits from an output a digital image of the microarray, and a processor that receives the digital image of the microarray from the scanner and then processes the digital image, identifying each of the microarray's sub-grids. The processor then detects in each of the sub-grids a center-representing pixel of a signal of a chemical material and an approximate radius of the signal. Then, the processor segments the signal and calculates a characterizing measure for the segmented signal.

Abstract: A method, apparatus, and computer program product for analyzing gene expressions is presented. An operation is performed for determining a gene expression pattern for a condition, wherein the gene expression pattern comprises a gene expression. Next, a spatial-expression pattern is formed by selecting a chromosomal region having an exon; and associating the gene expression within the gene expression pattern with its corresponding exon. A further operation may be performed, where in the forming of the spatial-expression pattern, a spatial-expression pattern signal is created as a representation of the spatial-expression pattern. The magnitude of the spatial-expression pattern signal at any point is determined by an expression level of the corresponding exon. Spatial patterns may be identified in the signal by means of various signal processing techniques such as Fourier or Wavelet transforms.

Abstract: A digital image processing-based system and method for quantitatively processing a plurality of nucleic acid species expressed in a microarray are disclosed. The microarray is a grid of a plurality of sub-grids of the nucleic acid species. The system includes a scanner that has a digital scanning sensor that scans the microarray and transmits from an output a digital image of the microarray, and a processor that receives the digital image of the microarray from the scanner and then processes the digital image, identifying each of the microarray's sub-grids. The processor then detects in each of the sub-grids a center-representing pixel of a signal of a chemical material and an approximate radius of the signal. Then, the processor segments the signal and calculates a characterizing measure for the segmented signal.

Abstract: An apparatus, method, and computer program product are provided for determining a confidence measure for the output of a process for assessing proteomic and genomic information samples. Typically, data is received as the results from a microarry experiment. The confidence measure is intended to determine whether the results of the experiment have been degraded due to experimental error. Several criteria are used by which quality is determined. The criteria are preferably combined into a combined quality measure in order to account for several possible sources of error.

Abstract: A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. The frame is stored in a memory device and a set of image information within said frame including a selected set of the DNA spot images is selected. A grid including a plurality of spaced grid points corresponding to said selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame.

Abstract: A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. A grid including a plurality of spaced grid points corresponding to selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame. For each DNA spot image: (1) background and signal intensity levels are extracted from image characteristic values for the spot image, and (2) difference values between the background intensity levels and signal intensity levels are determined. For each DNA spot: (1) the corresponding difference values are related a range of graphic values, (2) a graphic value for each difference value is selected; and (3) the selected graphic values are displayed.

Abstract: An apparatus, a method, and a computer program product for plotting proteomic and genomic data are presented. The apparatus comprises a computer system for generating data to display in a visual form. The computer system receives a set of proteomic and genomic data including data samples and schemes for partitioning the data samples into data partitions. Various operations are performed by the computer system in response to user commands, including adjusting the view of partition schemes in response to the selection of a particular partition scheme in order to allow a user to visually detect correlations among data. The system also allows for the performance of set operations on the proteomic and genomic data, and for displaying the results. Additionally, the computer system allows for operations for determining partition schemes and partitions in which a particular data sample are located, and for generating and modifying partition schemes.

Abstract: A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. The frame is stored in a memory device and a set of image information within said frame including a selected set of the DNA spot images is selected. A grid including a plurality of spaced grid points corresponding to said selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame.

Abstract: A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. The frame is stored in a memory device and a set of image information within said frame including a selected set of the DNA spot images is selected. A grid including a plurality of spaced grid points corresponding to said selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame.

Abstract: Systems and methods of analyzing data and for specifying and applying user-selected, user-variable sequences of mathematical data preparation operations to data and methods for normalizing data that include dividing the data into a plurality of groups where the number of groups is a function of the range and number of values and for calculating a normalization correction for each group are disclosed.

Abstract: A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. The frame is stored in a memory device and a set of image information within said frame including a selected set of the DNA spot images is selected. A grid including a plurality of spaced grid points corresponding to said selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame.