Clustering genes using gene expression and text literature data

Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005

Volumn 2005, Issue , 2005, Pages 329-340

  Yang, Chengyong ^a   Zeng, Erliang ^a   Li, Tao ^a   Narasimhan, Giri ^a  

^a The Department of Electrical and Computer Engineering   (United States)

Author keywords

Biological Literature; Gene Expression Data; Multi Source Clustering; Text Mining

Indexed keywords

ALGORITHMS; BIODIVERSITY; DATA MINING; DATA STRUCTURES; DATABASE SYSTEMS; GENES; INTEGRATION; MATHEMATICAL MODELS; PROBLEM SOLVING;

BIOLOGICAL LITERATURE; GENE EXPRESSION DATA; MULTI-SOURCE CLUSTERING; TEXT MINING;

GENETIC ENGINEERING;

PROTEOME;

ARTICLE; ARTIFICIAL INTELLIGENCE; CLASSIFICATION; CLUSTER ANALYSIS; DNA MICROARRAY; EVALUATION; GENE EXPRESSION PROFILING; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY; MULTIGENE FAMILY; NATURAL LANGUAGE PROCESSING; PHYSIOLOGY; PUBLICATION;

ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; INFORMATION STORAGE AND RETRIEVAL; MULTIGENE FAMILY; NATURAL LANGUAGE PROCESSING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PERIODICALS; PROTEOME;

EID: 33745496606     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2005.23     Document Type: Conference Paper

References (47)

1. Altman, R.B. and Raychaudhuri, S. (2001). "Whole-genome expression analysis: challenges beyond clustering." Current Opinion in Structural Biology 11(3): 340-347.
2. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G. and Consortium, G.O. (2000). "Gene Ontology: tool for the unification of biology." Nature Genetics 25(1): 25-29.
3. Baeza-Yates, R. and Ribeiro-Neto, B. (1999). Modern Information Retrieval, Addison Wesley Longman Publishing Co. Inc.
4. Ball, C.A., Brazma, A., Causton, H., Chervitz, S., Edgar, R., Hingamp, P., Matese, J.C., Parkinson, H., Quackenbush, J., Ringwald, M., Sansone, S.A., Sherlock, G., Spellman, P., Stoeckert, C., Tateno, Y., Taylor, R., White, J. and Winegarden, N. (2004). "Submission of microarray data to public repositories." PLoS Biol 2(9): E317.
5. Barbaric, S., Fascher, K.D. and Horz, W. (1992). "Activation of the weakly regulated PHO8 promoter in S. cerevisiae: chromatin transition and binding sites for the positive regulatory protein PHO4." Nucleic Acids Res 20(5): 1031-8.
6. Becker, S. (1996). "Mutual information maximization: Models of cortical self-organization." Network: Computation in Neural Systems 7(1): 7-31.
7. Ben-Dor, A., Shamir, R. and Yakhini, Z. (1999). "Clustering gene expression patterns." J Comput Biol 6(3-4): 281-97.
8. Berriz, G.F., King, O.D., Bryant, B., Sander, C. and Roth, P.P. (2003). "Characterizing gene sets with FuncAssociate." Bioinformatics 19(18): 2502-2504.
9. Bickel, S. and Tobias, S. (2004). Multi-View Clustering. Proceedings of the Fourth IEEE International Conference on Data Mining (ICDM'04).
10. Bozdech, Z., Llinas, M., Pulliam, B.L., Wong, E.D., Zhu, J.C. and DeRisi, J.L. (2003). "The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum." Plos Biology 1(1): 85-100.
11. Chaussabel, D. and Sher, A. (2002). "Mining microarray expression data by literature profiling." Genome Biol 3(10): RESEARCH0055.
12. Chiang, J.H. and Yu, H.C. (2003). "MeKE: discovering the functions of gene products from biomedical literature via sentence alignment." Bioinformatics 19(11): 1417-1422.
13. Dempster, A.P., Laird, N.M. and Rubin, D.B. (1977). "Maximum likelihood from incomplete data via the em algorithm." Journal of the Royal Statistical Society 39: 1-38.
14. Dolinski, K., Balakrishnan, R., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R., Fisk, D.G., Hirschman, I.E., Hong, E.L., Nash, R., Oughtred, R., Theesfeld, C.L., Binkley, G., Lane, C., Schroeder, M., Sethuraman, A., Dong, S., Weng, S., Miyasato, S., Andrada, R., Botstein, D. and Cherry, J.M. (2004). Saccharomyces Genome Database
15. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998). "Cluster analysis and display of genome-wide expression patterns." Proceedings of the National Academy of Sciences of the United States of America 95(25): 14863-14868.
16. Fleischmann, W., Moller, S., Gateau, A. and Apweiler, R. (1999). "A novel method for automatic functional annotation of proteins." Bioinformatics 15(3): 228-233.
17. Getz, G., Levine, E. and Domany, E. (2000). "Coupled two-way clustering analysis of gene microarray data." Proc Natl Acad Sci USA 97(22): 12079-84.
18. Gibbons, F.D. and Roth, F.P. (2002). "Judging the quality of gene expression-based clustering methods using gene annotation." Genome Research 12(10): 1574-1581.
19. Glenisson, P., Antal, P., Mathys, J., Moreau, Y. and De Moor, B. (2003). "Evaluation of the vector space representation in text-based gene clustering." Pac Symp Biocomput: 391-402.
20. Glenisson, P., Mathys, J. and De Moor, B. (2004). "Meta-Clustering of Gene Expression Data and Literature-based Information." SIGKDD Explorations 5(2): 101-112.
21. Gravano, L., Garcia-Molina, H. and Tomasic, A. (1999). "Gloss: Text-source discovery over the internet." ACM Transactions on Database Systems 24(2): 229-264.
22. Herwig, R., Poustka, A.J., Muller, C., Bull, C., Lehrach, H. and O'Brien, J. (1999). "Large-scale clustering of cDNA-fingerprinting data." Genome Research 9(11): 1093-1105.
23. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002). "Revealing modular organization in the yeast transcriptional network." Nature Genetics 31(4): 370-377.
24. Jain, A.K. and Dubes, R.C. (1988). Algorithms for clustering data, Prentice Hall.
25. Jenssen, T.K., Laegreid, A., Komorowski, J. and Hovig, E. (2001). "A literature network of human genes for high-throughput analysis of gene expression." Nat Genet 28(1): 21-8.
26. Kasturi, J. and Acharya, R. (2004). Clustering of diverse genomic data using information fusion Proceedings of the 2004 ACM symposium on Applied computing Nicosia, Cyprus ACM Press: 116-120
27. Masys, D.R. (2001). "Linking microarray data to the literature." Nat Genet 28(1): 9-10.
28. Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V., Kloos, D.-U., Land, S., Lewicki-Potapov, B., Michael, H., Munch, R., Reuter, I., Rotert, S., Saxel, H., Scheer, M., Thiele, S. and Wingender, E. (2003). "TRANSFAC(R): transcriptional regulation, from patterns to profiles." Nucl. Acids Res. 31(1): 374-378.
29. Neal, R.M. and Hinton, G. (1998). A view of the EM algorithm that justifies incremental, sparse, and other variants. Learning in Graphical Models. M. Jordan: 355-368.
30. Raghavan, V.V. and Wong, S.K.M. (1986). "A critical analysis of vector space model for information retrieval." Journal of the American Society for Information Science 37(5): 279-87.
31. Raychaudhuri, S., Chang, J.T., Imam, F. and Altman, R.B. (2003). "The computational analysis of scientific literature to define and recognize gene expression clusters." Nucleic Acids Research 31(15): 4553-4560.
32. Raychaudhuri, S., Chang, J.T., Sutphin, P.D. and Altman, R.B. (2002). "Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature." Genome Research 12(1): 203-214.
33. Roberts, R.J. (2001). "PubMed Central: The Gen-Bank of the published literature." Proc Natl Acad Sci U S A 98(2):381-2.
34. Roth, F.P., Hughes, J.D., Estep, P.W. and Church, G.M. (1998). "Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation." Nature Biotechnology 16(10): 939-945.
35. Segal, E., Yelensky, R. and Koller, D. (2003). "Genome-wide discovery of transcriptional modules from DNA sequence and gene expression." Bioinformatics 19 Suppl 1: 273-82.
36. Shatkay, H., Edwards, S., Wilbur, W. J. and Boguski, M. (2000). "Genes, themes and microarrays: using information retrieval for large-scale gene analysis." Proc Int Conf Intell Syst Mol Biol.
37. Sherlock, G. (2000). "Analysis of large-scale gene expression data." Current Opinion in Immunology 12(2): 201-205.
38. Spellman, P.T., Sherlock, G., Futcher, B., Brown, P.O. and Botstein, D. (1998). "Identification of cell cycle regulated genes in yeast by DNA microarray hybridization." Molecular Biology of the Cell 9:371a-371a.
39. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998). "Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization." Molecular Biology of the Cell 9(12): 3273-3297.
40. Stephens, M., Palakal, M., Mukhopadhyay, S., Raje, R. and Mostafa, J. (2001). Detecting gene relations from MEDLINE abstracts. Proc of the sixth Ann Pac Symp Biocomp (PSB 2001).
41. Tamames, J., Ouzounis, C., Casari, G., Sander, C. and Valencia, A. (1998). "EUCLID: automatic classification of proteins in functional classes by their database annotations." Bioinformatics 14(6): 542-543.
42. Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E.S. and Golub, T.R. (1999). "Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation." Proceedings of the National Academy of Sciences of the United States of America 96(6): 2907-2912.
43. Tanabe, L., Scherf, U., Smith, L.H., Lee, J.K., Hunter, L. and Weinstein, J.N. (1999). "Med-Miner: an Internet text-mining tool for biomedical information, with application to gene expression profiling." Biotechniques 27(6): 1210-4, 1216-7.
44. Vogel, K., Horz, W. and Hinnen, A. (1989). "The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 up-stream activation regions." Mol Cell Biol 9(5): 2050-7.
45. Wu, L., Oviatt, S.L. and Cohen, P.R. (1999). "Multimodal integration - a statistical view." IEEE Transactions on Multimedia 1(4): 334-341.
46. Yandell, M.D. and Majoras, W.H. (2002). "Genomics and natural language processing." Nature Reviews Genetics 3(8): 601-610.
47. Zhong, S. and Ghosh, J. (2003). "A comparative study of generative models for document clustering." Proceedings of the workshop on Clustering High Dimensional Data and Its Applications in SIAM Data Mining Conference.