Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-01-25
2005-01-25
Brusca, John S. (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
Reexamination Certificate
active
06847897
ABSTRACT:
A system, method, and computer program product for enhanced computer-aided analysis of biological response data is disclosed. In a preferred embodiment, biological datasets are graphically selected by a user from a first active biological viewer window on a user computer display and projected onto one or more other active biological viewers on the display. The selected data is highlighted in the destination biological viewers using contrast or color differentiation from other data appearing in the destination windows. In another preferred embodiment, hierarchical cluster trees from biological signal profiles are presented in a hyperbolic display fashion. In another preferred embodiment, biological menu and submenu items utilized by the user computer are not stored in the user computer, but rather are stored a central biological response database. Biological menus and submenus are generated at startup time based on queries to the central biological response database, allowing for increased flexibility, changeability, and customization of the biological menus. In another preferred embodiment, correlation data between biological signal profile data is precomputed when the experiments are added to the central biological response database, eliminating the need for real time computation of correlation coefficients by the user computer.
REFERENCES:
patent: 5510270 (1996-04-01), Fodor et al.
patent: 5556752 (1996-09-01), Lockhart et al.
patent: 5569588 (1996-10-01), Ashby et al.
patent: 5578832 (1996-11-01), Trulson et al.
patent: 5590250 (1996-12-01), Lamping et al.
patent: 5619632 (1997-04-01), Lamping et al.
patent: 5630125 (1997-05-01), Zellweger
patent: 5777888 (1998-07-01), Rine et al.
patent: 5966712 (1999-10-01), Sabatini et al.
patent: 5970500 (1999-10-01), Sabatini et al.
patent: 6043825 (2000-03-01), Glenn et al.
patent: 6165709 (2000-12-01), Friend et al.
patent: 6203987 (2001-03-01), Friend et al.
patent: 6300957 (2001-10-01), Rao et al.
patent: WO 9727317 (1996-01-01), None
patent: WO 9710365 (1996-09-01), None
patent: WO 9958720 (1999-11-01), None
Wen et al. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl. Acad. Sci. USA vol. 95, pp. 334-339 (1998).*
Wosikowski et al, Identification of Epidermal Growth Factor Receptor and c-erbB2 Pathway Inhibitors by Correlation With Gene Expression Paterns, Oct. 1997, Journal of the National Cancer Institute, vol. 89, No. 20, pp. 1505-1515.*
Duda and Hart, 1973,Pattern Classification and Scene Analysis, John Wiley & Sons, Inc., New York, pp. 211-256.
Michaels and Carr, 1998, “Cluster Analysis and Data Visualization of Large-Scale Gene Expression Data”, Pacific Symposium on Biocomputing 3:42-53.
Duda et al., 2001,Pattern Classification, John Wiley & Sons, Inc., New York, pp. 537-563.
Eisen et al., 1998, “Cluster analysis and display of genome-wide expression patterns”, Proc. Natl. Acad. Sci. USA 95: 14863-14868.
Blanchard et al., 1996, “Sequences to array: Probing the genome's secrets,”Nature Biotechnology 14:1649.
Blanchard et al., 1996, “High-Density Oligonucleotide Arrays,”Biosensors&Bioelectronics 11: 687-90.
Chee et al., 1996, “Accessing Genetic Information with High-Density DNA Arrays,”Science 274:610-614.
Chait, 1996, “Trawling for proteins in the post genome era,”Nat. Biotech. 14:1544.
DeRisi et al., 1996, “Use of a cDNA microarray to analyze gene expression patterns in human cancer,”Nature Genetics 14:457-460.
DeRisi et al., 1997, “Exploring the metabolic and genetic control of gene expression on a genomic scale,”Science 278:680-686.
Lamping and Rao, 1994, “Laying out and Visualizing Large Trees Using Hyperbolic Space,”UIST '94Nov. 2-4, 1994. Jul. 13, 1999Marina del Rey, California. pp. 13 and 14.
Lockhart et al., 1996, “Expression monitoring by hybridization to high-density oligonucleotide arrays,”Nature Biotechnology 14:1675-1680.
Marton et al., 1998, “Drug target validation and identification of secondary drug target effects using DNA microarrays,”Nat. Med. 4(11):1293-1301.
McCormack et al., 1997, “Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at low-femtomole level”,Anal. Chem. 69:767-776.
Schena et al., 1995, “Quantitative monitoring of gene expression patterns with a complementary DNA micro-array,”Science 270:467-470.
Schena et al., 1996, “Parallel human genome analysis; microarray-based expression monitoring of 1000 genes,”Proc. Natl. Acad. Sci. USA 93:10614-10619.
Shalon et al., 1996, “A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization,”Genome Res. 6:639-645.
Zhao et al., 1995, “High-density cDNA filter analysis: a novel approach for large-scale, quantitative analysis of gene expression,”Gene 156:207-213.
Bassett, Jr. Douglas
Bondarenko Andrey
Brusca John S.
Jones Day
Rosetta Inpharmatics LLC
LandOfFree
Method and system for analyzing biological response signal data does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Method and system for analyzing biological response signal data, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method and system for analyzing biological response signal data will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3389778