System, methods, and computer program product for analyzing...

Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

Reexamination Certificate

active

09934156

ABSTRACT:
The present invention relates to systems, methods, and computer program products for the analysis of gene expression data, especially data that have been acquired using microarray technologies. The present invention relates to methods for partitioning a set of genes into clusters, based on the similarity of the genes' rates of messenger RNA synthesis. The present invention also relates to methods for annotating clusters with words or phrases that are extracted from documents associated with genes in the clusters. The present invention also relates to methods for evaluating the quality of clustering based on the extend to which documents associated with genes in a cluster collectively distinguish that cluster from all the other clusters, as well as the extent to which some words and phrases, present in documents associated with genes in the cluster, collectively distinguish that cluster from all the other clusters.

REFERENCES:
patent: 6245517 (2001-06-01), Chen et al.
patent: 6263287 (2001-07-01), Zheng et al.
Andrade et al., Bioinformatics, vol. 15, pp. 391-412, 1999.
McCallum, www-2.cs.cmu.edu/˜mccallum/bow/rainbow, pp. 1-11, 1998.
Benson et al., Nucleic Acids Research, vol. 25, pp. 1-6, 1997.
Bairoch et al., Nucleic Acids Research, vol. 25, pp. 217-221, 1997.
Duggan, D.J., M. Bittner, Y. Chen, P. Meltzer and J.M. Trent. Expression profiling using cDNA arrays. Nature Genetics 21, Suppl 1: 10-14 (1999).
Newton, M.A., C.M. Kendziorski, C.S. Richmond, F.R. Blattner, and K.W. Tsui. On differential variability of expression ratios. Tech. Rept. 139, Dept. of Biostatistics, Univ. of Wisconsin-Madison. http://www.stat.wisc.edu/˜newton/papers/publications (1999).
Iyer, V.R., M.B. Eisen, D.T. Ross, G. Schuler, T. Moore, J.C.F. Lee, J.M. Trent, L.M. Staudt, J. Hudson Jr., M.S. Boguski, D. Lashkari, D. Shalon, D. Botstein and P.O. Brown. The transcriptional program in the response of human fibroblasts to serum. Science 283: 83-87 (1999).
Eisen, M.B, P.T. Spellman, P.O. Brown and D. Botstein. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868 (1998).
Tavazoie, S., J.D. Hughes, M.J. Campbell, R.J. Cho, and J.M. Church. Systematic determination of genetic network architecture. Nature Genetics 22:281-285 (1999).
Tamayo, P, D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E.S. Lander, and T.R. Golub. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96: 2907-2912 (1999).
Ben-Dor, A., R. Shamir and Z. Yakhini. Clustering gene expression patterns. J. Computational Biology 6:281-297 (1999).
Getz, G., E. Levine, E. Domany, and M.Q. Zhang. Super-paramagnetic clustering of yeast gene expression profiles. arXiv:physics/9911038 at preprint server xxx.lanl.gov (1999).
Perou, C.M., S.S. Jeffrey, M. van de Rijn, C.A. Rees, M.B. Eisen, D.T. Ross, A. Pergamenschikov, C.F. Williams, S.X. Zhu, D. et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA 96: 9212-9217 (1999).
Tibshirani, R., T. Hastie, M. Eisen, D. Ross, D. Botstein, and P. Brown. Clustering methods for the analysis of DNA microarray data. Manuscript from Web site http://www-stat.stanford.edu/˜tibs/lab/publications.html (1999).
Kaufman, L. and P.J. Rousseeuw. Finding Groups in Data: An Introduction to Cluster Analysis. New York: Wiley (1990).
Holmes, I. and W.J. Bruno. Finding regulatory elements using joint likelihoods for sequence and expression profile data. Proc. Eighth International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park CA, pp. 202-210. (2000).
Yeung, K.Y., D.R. Haynor and W.L. Ruzzo. Validating clustering for gene expression data. Technical report UW-CSE-00-01-01. University of Washington, Seattle. Manuscript from Web site http://www.cs.washington.edu/homes/kayee/research.html (2000).
Shatkay, H., S. Edwards, W.J. Wilbur, and M. Boguski. Genes, themes, and microarrays. Using information retrieval for large-scale gene analysis. Proc. Eighth International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park CA, pp. 317-328. (2000).
Masys, D.R., J.B. Welsh, J.L. Fink, M. Gribskov, I. Klacansky, and J. Corbeil. Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics 17: 319-326 (2001).
Delorie, D.J. Guide: What is DJGPP? Web page from http://www.delorie.com//djgpp/doc/ug/intro/what-is-djpp.html (1997).
McCallum, A.K. Rainbow. Web page from http://www.cs.cmu.edu/˜mccallum.bow (1998).
Press, W.H., S.A. Teukolsky, W.T. Vetterling, and B.P. Flannery. Numerical Recipes in C. The Art of Scientific Computing, Second. edn. New York: Cambridge University Press (1992).
Manning, C.D. and H. Schutze. Foundations of Statistical Natural Language Processing. Cambridge MA: The MIT Press (1999).
Mitchell, T. Machine Learning. New York: McGraw-Hill (1997).
Egghe, L. and R. Rousseau. Introduction to Informetrics. Quantitative Methods in Library, Documentation, and Information Science. Amsterdam: Elsevier Science Publishers (1990).
Sonnhammer, E.L.L., S.R. Eddy, and R. Durbin. Pfam: a comprehensive database of protein domain families based on seed alignments. PROTEINS 28: 405-420 (1997).
Tamames, J., C. Ouzounis, G. Casari, C. Sander, and A. Valencia. EUCLID: automatic clasification of proteins in functional classes by their database annotations. Bioinformatics 14: 542-543 (1998).
Andrade, M.A. and A. Valencia. Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. Bioinformatics 14: 600-607 (1998).
Chaussabel, D. and A. Sher. Mining microarray expression data by literature profiling Genome Biology 2002, 3(10):research0055.1-0055.16 (2002).
Butler, B.A. Sequence analysis using GCG, Chapter 4 (pp. 74-97) in A.D.Baxevanis and B.F.F. Ouellette, eds. Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins. New York: Wiley Interscience, 1998.

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

System, methods, and computer program product for analyzing... 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, methods, and computer program product for analyzing..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and System, methods, and computer program product for analyzing... will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-3853903

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.