Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2008-07-29
2008-07-29
Zhou, Shubo (Joe) (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C703S011000, C707S793000
Reexamination Certificate
active
10330007
ABSTRACT:
A system and method for identifying high order associations between variables in complex systems that is particularly useful where there is no correlation or weak correlation between variables due to the influence of a third variable, a ternary relationship. The ternary relationship describes how the variation in the pattern of association between a pair of variables, including its sign and strength, is mediated by a third variable. In one embodiment applied to gene expression data, the activity of pairs of correlated genes due to the activity of one or more third genes is shown.
REFERENCES:
patent: 6420105 (2002-07-01), Landfield et al.
patent: 6421668 (2002-07-01), Yakhini et al.
Qian et al., JMB, vol. 314, pp. 1053-1066, 2001.
YM Seminar Anouncement, printed on Sep. 14, 2005 from the internet <http://binfo.ym.edu.tw/edu/seminars/seminar92—2.htm>.
NUK Talk, a seminar anouncement, printed on Sep. 13, 2005 from the internet <http://stat.nuk.edu.tw/talk/92-2.htm>.
Merriam-Webster Online, definition for “stagger”, < http://www.m-w.com/cgi-bin/dictionary?book=Dictionary&va=stagger>.
Li et al. Proc. Natl. Acad. Sci. USA, 2004, vol. 101, pp. 15561-15566. See Pubmed Abstract.
Li, K-C, Proc. Natl. Acad. Sci. USA, vol. 99, pp. 16875-16880, 2002.
Proc. Natl. Acad. Sci. Online Publication Notice, retrieved from http://www.pnas.org/cgi/content/full/99/26/16875?ijkey=82b374df17d4c59a4a815d29d49dc00a7b9a94e0 on Jun. 8, 2006.
Li, Ker-Chau et al.; “The Data-Smoothing Aspect of Stein Estimates,” The Annals of Statistics, vol. 12, No. 3, pp. 887-897, (1984).
Li, Ker-Chau; “From Stein's Unbiased Risk Estimates to the Method of Generalized Cross Validation,” The Annals of Statistics, vol. 13, No. 4, pp. 1352-1377, (1985).
Li, Ker-Chau et al.; “A Simple Statistical Model for Depicting the CDC15-Synchronized Yeast Cell-Cycle Regulated Gene Expression Data,” Statistica Sinica, vol. 12, No. 1, pp. 141-158, Jan. 2002.
Li, Ker-Chau et al.; “Sliced Inverse Regression for Dimension Reduction,” Journal of the American Statistical Association, vol. 86, No. 414, pp. 316-342, Jun. 1991.
Li, Ker-Chau et al.; “Dimension Reduction for Multivariate Response Data,” Work in Progress, pp. 1 thru 26 with 11 pages of figures, Feb. 5, 2002.
Li, Ker-Chau et al.; “A Bayesian Insertion/Deletion Robust Algorithm for Distant Protein Motif Searching Via Entropy Filtering,” Work in Progress, pp. 1 thru 38, Sep. 27, 2000.
Li, Ker-Chau; “On Principal Hessian Directions for Data Visualization and Dimension Reduction: Another Application of Stein's Lemma,” Journal of the American Statistical Association, vol. 87, No. 420, pp. 1025-1039, Dec. 1992.
Babler, Jochen et al.; “Identification of a 60S Preribosomal Particle That is Closely Linked to Nuclear Export,” Molecular Cell, vol. 8, pp. 517-529, Sep. 2001.
Shore, Paul et al.; “The Mads-Box Family of Transcription Factors,” Journal of Biochemistry, vol. 229, pp. 1-13, (1995).
Grotzinger, C. et al.; “Li-Cadherin: A Marker of Gastric Metaplasia and Neoplasia,” Gut Journal, vol. 49, pp. 73-81, (2001).
Myeroff, Lois L. et al.; Increased NM23-H1 and NM23-H2 Messenger RNA Expression and Absence of Mutations in Colon Carcinomas of Low and High Metastatic Potential, Journal of the National Cancer Institute, vol. 85, No. 2, pp. 147-152, Jan. 20, 1993.
DuBois, E. et al.; “Integration of the Multiple Controls Regulating the Expression of the Arginase Genecar1ofSaccharomyces cerevisiaein Response to Different Nitrogen Signals: Role of Gln3p, ArgRp-Mem1p, and Ume6p,” Mol. Gen. Genet, vol. 253, pp. 568-580, (1997).
Martinez, J.A. et al.; “Overexpression of nm23-H1 and nm23-H2 Genes in Colorectal Carcinomas and Loss of nm23-H1 Expression in Advanced Tumour Stages,” Gut Journal, vol. 37, pp. 712-720, (1995).
Carter, A.T. et al.; “PRS1 is a Key Member of the Gene Family Encoding Phosphoribosylpyrophosphate Synthetase inSaacharomyces cerevisiae,” Mol. Gen. Genet. vol. 254, pp. 148-156, (1997).
Weaver, Robert; “Molecular Biology-Second Edition,” Cover page, Title page, pp. 406-407, McGraw-Hill Companies, (2002).
Alberts, Bruce et al.; “Molecular Biology of the Cell-Third Edition,” Cover page, Title page, pp. 47, Garland Publishing, (1994).
Voet, Donald et al.; “Biochemistry-Second Edition,” Cover page, Title page, pp. 472, John Wiley & Sons, (1995).
Lodish, Harvey et al.; “Molecular Cell Biology-Third Edition,” Cover page, Title page, pp. 771, Scientific American Books, (1995).
Cook, R. Dennis et al.; “Reweighting to Achieve Elliptically Contoured Covariates in Regression,” Journal of the American Statistical Association, vol. 89, No. 426, pp. 592-599, (1994).
Cook, R. Dennis; “Regression Graphics,” Cover page, Title page, pp. 224-228, John Wiley & Sons, (1998).
Molenaar, I.W. et al. (eds.); “Encyclopedia of Statistical Sciences-vol. 6,” Multivariate Analysis to Plackett and Burman Designs, Cover page, Title page, pp. 347-367, (1982).
Molenaar, I.W. et al. (eds.); “Encyclopedia of Statistical Sciences-vol. 2,” Classification to Eye Estimate, Cover page, Title page, pp. 193-204, (1982).
Morrison, Donald F.; “Multivariate Statistical Methods-Third Edition,” Cover page, Title page, pp. 90-94, (1990).
Li, Ker-Chau; “Genome-Wide Coexpression Dynamics: Theory and Application,” PNAS, vol. 99, No. 26, pp. 16875-16880, Dec. 24, 2002.
Clancy, David J. et al.; “Extension of Life-Span by Loss of Chico, aDrosophilaInsulin Receptor Substrate Protein,” Science, vol. 292, pp. 104-106, Apr. 6, 2001.
Bijlani, Rahul et al.; “Prediction of Biologicall Significant Components From Microarray Data: Independently Consistent Expression Discriminator(iced),” Bioinformatics, vol. 19, No. 1, pp. 62-70, (2003).
Staunton, Jane E. et al.; “Chemosensitivity Prediction by Transcriptional Profiling,” PNAS, vol. 98, No. 19, pp. 10787-10792, Sep. 11, 2001.
Orr, M.S. et al.; “Large-Scale Gene Expression Analysis in Molecular Target Discovery,” Leukemia, vol. 16, pp. 473-477, (2002).
Ashburner, Michael et al.; “Gene Ontology: Tool for the Unification of Biology,” Nature Genetics, vol. 25, pp. 25-29, May 2000.
Golub, T.R. et al.; “Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring,” Science, vol. 286, p. 531-537, Oct. 15, 1999.
Hazbun, Tony R. et al.; “Networking Proteins in Yeast,” PNAS, vol. 98, No. 8, pp. 4277-4278, Apr. 10, 2001.
Holter, Neal S. et al.; “Fundamental Patterns Underlying Gene Expression Profiles: Simplicity From Complexity,” PNAS, vol. 97, No. 15, pp. 8409-8414, Jul. 19, 2000.
Jiang, Cecilia H. et al.; “The Effects of Aging on Gene Expression in the Hypothalamus and Cortex of Mice,” PNAS, vol. 98, No. 4, pp. 1930-1934, Feb. 13, 2001.
Lee, Cheol-Koo et al.; “Gene Expression Profile of Aging and its Retardation by Caloric Restriction,” Science, vol. 285, pp. 1390-1393, Aug. 27, 1999.
Quackenbush, John; “Microarray Data Normalization and Transformation,” Nature Genetics Supplement, vol. 32, pp. 496-501, Dec. 2002.
Banerjee, Debabrata et al.; “Novel Aspects of Resistance to Drugs Targeted to Dihydrofolate Reductase and Thymidylate Synthase,” Biochimica et Biophysica Acts, vol. 1587, pp. 164-173, (2002).
Gailus-Durner, Valerie et al.; “Experimental Data of a Single Promoter Can be Used for In Silico Detetion of Genes With Related Regulation in the Absence of Sequence Similarity,” Mammalian Genome, vol. 12, pp. 67-72, (2001).
Ross, Douglas T. et al.; “Systemactic Variation in Gene Expression Patterns in Human Cancer Cell Lines,” Nature Genetics, vol. 24, pp. 227-235, Mar. 2000.
Zhou, Xianghong et al
O'Banion John P.
The Regents Of The University Of California
Zhou Shubo (Joe)
LandOfFree
System and method for identifying networks or ternary... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with System and method for identifying networks or ternary..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and System and method for identifying networks or ternary... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3919940