Text mining biomedical literature for discovering gene-to-gene relationships: A comparative study of algorithms

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 2, Issue 1, 2005, Pages 62-75

  Liu, Ying ^a   Navathe, Shamkant B ^a   Civera, Jorge ^a   Dasigi, Venu ^b   Ram, Ashwin ^a   Ciliax, Brian J ^c   Dingledine, Ray ^c  

^a Georgia Institute of Technology   (United States)

^b SOUTHERN POLYTECHNIC STATE UNIVERSITY   (United States)

^c EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Bond energy algorithm; Cluster analysis; Gene function; MEDLINE; Microarray; Text analysis

Indexed keywords

BOND ENERGY ALGORITHMS; CLUSTER ANALYSIS; GENE FUNCTION; MEDLINE; MICROARRAY; TEXT ANALYSIS;

ALGORITHMS; BIOASSAY; BIOMEDICAL ENGINEERING; CHEMICAL BONDS; DNA; PROBLEM SOLVING;

GENES;

PROTEIN;

ALGORITHM; ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; DOCUMENTATION; EVALUATION; GENE EXPRESSION PROFILING; INFORMATION RETRIEVAL; LINGUISTICS; MEDLINE; METABOLISM; METHODOLOGY; MULTIGENE FAMILY; NATURAL LANGUAGE PROCESSING; PHYSIOLOGY; PROTEIN ANALYSIS; PUBLICATION;

ABSTRACTING AND INDEXING; ALGORITHMS; GENE EXPRESSION PROFILING; INFORMATION STORAGE AND RETRIEVAL; MEDLINE; MULTIGENE FAMILY; NATURAL LANGUAGE PROCESSING; PERIODICALS; PROTEIN INTERACTION MAPPING; PROTEINS; VOCABULARY, CONTROLLED;

EID: 19944381853     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2005.14     Document Type: Article

References (28)

1. C. Blaschke, J.C. Oliveros, and A. Valencia, "Mining Functional Information Associated with Expression Arrays," Functional & Integrative Genomics, vol. 1, pp. 256-268, 2001.
2. Y. Xu, V. Olman, and D. Xu, "EXCAVATOR: A Computer Program for Efficiently Mining Gene Expression Data," Nucleic Acids Research, vol. 31, pp. 5582-5589, 2003.
3. D. Chaussabel and A. Sher, "Mining Microarray Expression Data by Literature Profiling," Genome Biology, vol. 3, pp. 1-16, 2002.
4. V. Cherepinsky, J. Feng, M. Rejali, and B. Mishra, "Shrinkage-Based Similarity Metric for Cluster Analysis of Microarray Data," Proc. Nat'l Academy of Sciences USA, vol. 100, pp. 9668-9673, 2003.
5. J. Quackenbush, "Computational Analysis of Microarray Data," Nature Rev. Genetics, vol. 2, pp. 418-427, 2001.
6. M.B. Eisen, P.T. Spellman, P.O. Brown, and D. Botstein, "Cluster Analysis and Display of Genome-Wide Expression Patterns," Proc. Nat'l Academy of Sciences USA, vol. 95, pp. 14863-14868, 1998.
7. R. Herwig, A.J. Poustka, C. Mller, C. Bull, H. Lehrach, and J. O'Brien, "Large-Scale Clustering of cDNA-Fingerprinting Data," Genome Research, vol. 9, pp. 1093-1105, 1999.
8. P. Tamayo, 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. Nat'l Academy of Sciences USA, vol. 96, pp. 2907-2912, 1999.
9. A.K. Jain, M.N. Murty, and P.J. Flynn, "Data Clustering: A Review," ACM Computing Surveys, vol. 31, pp. 264-323, 1999.
10. S. Raychaudhuri, J.T. Chang, F. Imam, and R.B. Altman, "The Computational Analysis of Scientific Literature to Define and Recognize Gene Expression Clusters," Nucleic Acids Research, vol. 15, pp. 4553-4560, 2003.
11. B. Kegl, "Principle Curves: Learning, Design, and Applications," PhD dissertation, Dept. of Computer Science, Concordia Univ., Montreal, Quebec, 2002.
12. T.K. Jenssen, A. Laegreid, J. Komorowski, and E. Hovig, "A Literature Network of Human Genes for High-Throughtput Analysis of Gene Expression," Nat'l Genetics, vol. 178, pp. 139-143, 2001.
13. D.R. Masys, J.B. Welsh, J.L. Fink, M. Gribskov, I. Klacansky, and J. Corbeil, "Use of Keyword Hierarchies to Interprate Gene Expression Patterns," Bioinformatics, vol. 17, pp. 319-326, 2001.
14. S. Raychaudhuri, H. Schutze, and R.B. Altman, "Using Text Analysis to Identify Functionally Coherent Gene Groups," Genome Research, vol. 12, pp. 1582-1590, 2002.
15. M. Andrade and A. Valencia, "Automatic Extraction of Keywords from Scientific Text: Application to the Knowledge Domain of Protein Families," Bioinformatics, vol. 14, pp. 600-607, 1998.
16. W.T. McCormick, P.J. Schweitzer, and T.W. White, "Problem Decomposition and Data Reorganization by a Clustering Technique," Operations Research, vol. 20, pp. 993-1009, 1972.
17. S. Navathe, S. Ceri, G. Wiederhold, and J. Dou, "Vertical Partitioning Algorithms for Database Design," ACM Trans. Database Systems, vol. 9, pp. 680-710, 1984.
18. P. Arabie and L.J. Hubert, "The Bond Energy Algorithm Revisited," IEEE Trans. Systems, Man, and Cybernetics, vol. 20, pp. 268-274, 1990.
19. A.T. Ozsu and P. Valduriez, Principles of Distributed Database Systems, second ed. Prentice Hall Inc., 1999.
20. Y. Liu, M. Brandon, S. Navathe, R. Dingledine, and B.J. Ciliax, "Text Mining Functional Keywords Associated with Genes," Proc. Medinfo 2004, pp. 292-296, Sept. 2004.
21. Y. Liu, B.J. Ciliax, K. Borges, V. Dasigi, A. Ram, S. Navathe, and R. Dingledine, "Comparison of Two Schemes for Automatic Keyword Extraction from MEDLINE for Functional Gene Clustering," Proc. IEEE Computational Systems Bioinformatics Conf. (CSB 2004), pp. 394-404, Aug. 2004.
22. P. Cheeseman and J. Stutz, "Bayesian Classification (Autoclass): Theory and Results," Advances in Knowledge Discovery and Data Mining, pp. 153-180, AAAI/MIT Press, 1996.
23. A. Strehl, "Relationship-Based Clustering and Cluster Ensembles for High-Dimensional Data Mining," PhD dissertation, Dept. of Electric and Computer Eng., The University of Texas at Austin, 2002.
24. R. Baeza-Yates and B. Ribeiro-Neto, Modern Information Retrieval. New York: Addison Wesley Longman, 1999.
25. F. Sebastiani, "Machine Learning in Automated Text Categorization," ACM Computing Surveys, vol. 34, pp. 1-47, 1999.
26. P. Willett, "Recent Trends in Hierarchic Document Clustering: A Critical Review," Information Processing and Management, vol. 24, pp. 577-597, 1988.
27. J. Aslam, A. Leblanc, and C. Stein, "Clustering Data without Prior Knowledge," Proc. Algorithm Eng.: Fourth Int'l Workshop, 1982.
28. P.V. Balakrishnan, M.C. Cooper, V.S. Jacob, and P.A. Lewis, "A Study of the Classification Capabilities of Neural Networks Using Unsupervised Learning: A Comparison with K-Means Clustering," Psychometrika, vol. 59, pp. 509-525, 1994.