Gene discovery for the system assignment of gene function

Details Gene discovery for the system assignment of gene function Gene discovery for the system assignment of gene function

2002-01-31

2009-11-24

Smith, Carolyn L. (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C702S020000, C703S011000, C707S793000, C435S006120, C435S007100

Reexamination Certificate

active

07623969

ABSTRACT:
The invention provides a method for assigning a cellular function to a component of a biochemical system. The method involves (a) determining a multidimensional shape space for one or more components of a biochemical system in a reference state; (b) perturbing a component within said biochemical system; (c) determining a perturbed multidimensional shape space for one or more components of a pathway in said perturbed biochemical system, and (d) identifying a multidimensional coordinate point corresponding to a component of said perturbed pathway altered between reference and perturbed multidimensional shape spaces, said identified component being assigned a cellular function of said perturbed pathway.

REFERENCES:
patent: 5814445 (1998-09-01), Belyavsky et al.
patent: 5980096 (1999-11-01), Thalhammer-Reyero
patent: 6132969 (2000-10-01), Stoughton et al.
patent: 6188988 (2001-02-01), Barry et al.
patent: 6194217 (2001-02-01), Matson
patent: 6203987 (2001-03-01), Friend et al.
patent: 6287765 (2001-09-01), Cubicciotti
patent: 7343247 (2008-03-01), Hood et al.
patent: 2001/0034580 (2001-10-01), Skolnick et al.
patent: 2001/0044699 (2001-11-01), Ewing et al.
patent: WO 99/11822 (1999-03-01), None
patent: WO 99/57130 (1999-11-01), None
patent: WO 00/11208 (2000-03-01), None
patent: WO 00/45322 (2000-08-01), None
Aebersold et al., “Equipping scientists for the new biology,”Nature Biotechnology18:359 (2000).
Alper J., “Weighing DNA for fast genetic diagnosis,”Science279:2044-2045 (1998).
Anderson,An Introduction to Multivariate Statistical Analysis, second ed., chapter 6, pp. 195-243 Wiley, New York (1984).
Burton and Hardíng, “Hydrophobic charge induction chromatography: salt independent protein adsorption and facile elution with aqueous buffers,”J. Chromatography814:71-81 (1998).
Cheng and Church, “Biclustering of Expression Data,”Proc. Int. Conf. Intell. Syst. Mol. Biol.8:93-103 (2000).
Eichler et al., “Peptide, peptidomimetic, and organic synthetic combinatorial libraries,”Med. Res. Rev.15:481-496 (1995).
Eisenberg et al., “Protein function in the post-genomic era,”Nature405:823-826 (2000).
Ellington and Szostak, “In vitro selection of RNA molecules that bind specific ligands,”Nature346:818-822 (1990).
Emili and Cagney, “Large-scale functional analysis using peptide or protein arrays,”Nature Biotech.18:393-397 (2000).
Fellenberg et al., “Integrative Analysis of Protein Interaction Data,”Proc. Int. Cont. Intell. Syst. Mol. Biol.8:152-161 (2000).
Famulok M., “Oligonucleotide aptamers that recognize small molecules,”Current Opinion in Structural Biology9:324-329 (1999).
Famulok and Mayer, “Aptamers as tools in molecular biology and immunolgoy,”Curr. Top. Microbiol. Immunol.243:123-136 (1999).
Fang et al., “Designing a novel molecular beacon for surface-immobilized DNA hybridization studies,”J. Am. Chem. Soc.121:2921-2922 (1999).
Fang et al., “Single and multiple molecular beacon probes for DNA hybridization studies on a silica glass surface,”SPIE3602:149-155 (1999).
Francis et al., “Combinatorial libraries of transition-metal complexes, catalysts and materials,”Curr. Opin. Chem. Biol.2:422-428 (1998).
Freund and Schapire, “A decision-theoretic generalization of on-line learning and an application to boosting,”J. Computer System Sciences55:119-139 (1997).
“Gene Logic and Fujisawa Pharmaceutical sign collaborative discovery research alliance; companies to identify gene expression profiles for diabetes therapeutics,” www.genelogic.com, Dec. 2, 1999.
Gold et al., “Diversity of oligonucleotide functions,”Annu. Rev. Biochem.64:763-797 (1995).
Golub et al., “Molecular classification of cancer: class discovery and class prediction by gene expression monitoring,”Science286:531-537 (1999).
Gygi et al., “Quantitative analysis of complex protein mixtures using isotope-coded affinity tags,”Nature Biotechnol.17:994-999 (1999).
Hermann and Patel, “Adaptive recognition by nucleic acid aptamers,”Science287:820-825 (2000).
Hollstein et al.,“p53 mutations in human cancers,”Science253:49-53 (1991).
Hughes et al., “Functional discovery via a compendium of expression profiles,”Cell102:109-126 (2000).
Ideker, T.,“Statement of Research Interests” (Fall 2000).
Jayasena S., “Aptamers: an emerging class of molecules that rival antibodies in diagnostics,”Clin.Chem.45:1628-1650 (1999).
Joyce G.,“In vitro evolution of nucleic acids,”Curr. Opin. Struct. Biol.4:331-336 (1994).
Kuffner et al., “Pathway analysis in metabolic data bases via differential metabolic display (DMD),”Bioinformatics16:825-836 (2000).
Li and Breaker, “Deoxyribozymes: new players in the ancient game of biocatalysis,”Current Opinion in Structural Biology9:315-323 (1999).
Lockhart & Winzeler, “Genomics, gene expression and DNA arrays,”Nature405:827-836 (2000).
Lorsch and Szostak, “Chance and necessity in the selection of nucleic acid catalysts,”Acc. Chem. Res.29:103-110 (1996).
Marcotte et al., “A combined algorithm for genome-wide prediction of protein function,”Nature402:83-86 (1999).
Proux et al., “A pragmatic information extraction strategy for gathering data on genetic interactions,”Proc. Int. Conf. Intell. Syst. Mol. Biol.8:279-285 (2000).
Schwikowski et al., “A network of protein—protein interactions in yeast,”Nature Biotechnol.18:1257-1261(2000).
Sofia M., “Carbohydrate-based combinatorial libraries,”Mol. Divers.2:75-94 (1998).
Sutcliffe et al., “Toga: An automated parsing technology for analyzing expression of nearly all genes,”Proc. Natl. Acad. Sci. USA97:1976-1981 (2000).
Suzuki et al., “Insulin resistance associated with decreased levels of insulin-receptor messenger ribonucleic acid: evidence of a de novo mutation in the maternal allele,”J. Clin. Endocrinol. Metab.80:1214-1220 (1995).
Taira et al., “Human diabetes associated with a deletion of the tryosine kinase domain of the insulin receptor,”Science245:63-66 (1989).
Taylor S., “Lilly lecture: molecular mechanisms of insulin resistance,”Diabetes41:1473-1490 (1992).
Tietz Textbook Clinical Chemistry, 2nd ed., Burtis and Ashwood, eds., W.B. Saunders Co., Philadelphia, pp. 958-984, 992-997, 1053-1087, 1211-1228, 1320-1350, 1354-1372, 1743-1772, 1887-1913 and 2059-2066 (1994).
Tietz Textbook Clinical Chemistry, 3rd ed., Burtis and Ashwood, eds., W.B. Saunders Co., Phildelphia, Chapters 2 and 11-14, pp. 42-72 and 265-355 (1999).
Tohsato et al., “A multiple alignment algoithm for metabolic pathway analysis using enzyme hierarchy,”Proc. Int. Conf. Intell. Syst. Mol. Biol.8:376-383 (2000).
Tokino and Nakamura, “The role of p53-target genes in human cancer,”Critical Reviews in Oncology/Hematology33:1-6 (2000).
Tuerk and Gold, “Systematic evolution of ligands by exponential enrichment: RNA ligands to T4 DNA polymerase,”Science249:505-510 (1990).
van Someren et al., “Linear modeling of genetic networks from experimental data,”Proc. Int. Conf. Intell. Syst. Mol. Biol.8:355-366 (2000).
Walt D., “Bead-based fiber-optic arrays,”Science287:451-452 (2000).
Wang X., “Role of p53 and apoptosis in carcinogenesis,”Anticancer Research19:4759-4771 (1999).
Yona and Levitt, “Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins,”Proc. Int. Conf. Intell. Syst. Mol. Biol.8:395-406 (2000).
Zien et al., “Analysis of Gene Expression Data with pathway scores,”Proc. Int. Conf. Intell. Syst. Mol. Biol.8:407-417 (2000).
Timecourse Data: Metabolic Chart, http://cmgm.stanford.edu/pbrown/explore/metachart.html: pp. 1-2 (

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