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Vol. 11, No. 6, 2004
Issue release date: November–December 2004
J Biomed Sci 2004;11:864–873

TransMiner: Mining Transitive Associations among Biological Objects from Text

Narayanasamy V. · Mukhopadhyay S. · Palakal M. · Potter D.A.
aSchool of Informatics, bDepartment of Computer and Information Science, and cDepartments of Medicine and Biochemistry and Walther Oncology Center, Indiana University School of Medicine, Indiana University Purdue University Indianapolis, Ind., USA

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Associations among biological objects such as genes, proteins, and drugs can be discovered automatically from the scientific literature. TransMiner is a system for finding associations among objects by mining the Medline database of the scientific literature. The direct associations among the objects are discovered based on the principle of co-occurrence in the form of an association graph. The principle of transitive closure is applied to the association graph to find potential transitive associations. The potential transitive associations that are indeed direct are discovered by iterative retrieval and mining of the Medline documents. Those associations that are not found explicitly in the entire Medline database are transitive associations and are the candidates for hypothesis generation. The transitive associations were ranked based on the sum of weight of terms that co-occur with both the objects. The direct and transitive associations are visualized using a graph visualization applet. TransMiner was tested by finding associations among 56 breast cancer genes and among 24 objects in the calpain signal transduction pathway. TransMiner was also used to rediscover associations between magnesium and migraine.

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  1. Baasiri RA, Glasser SR, Steffen DL, Wheeler DA. The Breast Cancer Gene Database: A collaborative information resource. Oncogene 18:7958–7965;1999.$tsrchname?Name = &topic = BCIR.
  2. Bao JJ, Le XF, Wang RY, Yuan J, Wang L, Atkinson EN, LaPushin R, Andreeff M, Fang B, Yu Y, Bast, RC Jr. Reexpression of the tumor suppressor gene ARHI induces apoptosis in ovarian and breast cancer cells through a caspase-independent calpain dependent pathway. Cancer Res 62:7264–7272;2002.
  3. Cuevas BD, Abell AN, Witowsky JA, Yujiri T, Johnson NL, Kesavan K, Ware M, Jones PL, Weed SA, DeBiasi RL, Oka Y, Tyler KL, Johnson GL. MEKK1 regulates calpain-dependent proteolysis of focal adhesion proteins for rear-end detachment of migrating fibroblasts. EMBO J 22:3346–3355;2003.
  4. Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I. Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics 20:604–611;2004.
  5. Demirkaya S, Vural O, Dora B, Topcuoglu MA. Efficacy of intravenous magnesium sulfate in the treatment of acute migraine attacks. Headache 41:171–177;2001.
  6. Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17(suppl 1):S74–S82;2001.
  7. Honderich T. The Oxford Companion to Philosophy, Oxford University Press. 1995
  8. Hristovski D, Dzeroski S, Peterlin B, Rozic-Hristovski A. Supporting Discovery in Medicine by Association Rule Mining of Bibliographic Databases. Proc Fourth European Conference on Principles and Practice of Knowledge Discovery in Databases. Berlin, Springer, 446–451;2000.
  9. Jenssen TK, Laegreid A, Komorowski J, Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nature Genetics 28:21–28;2000.
  10. Mathiasen IS, Sergeev IN, Bastholm L, Elling F, Norman AW, Jaattela M. Calcium and calpain as key mediators of apoptosis-like death induced by vitamin D compounds in breast cancer cells. J Biol Chem 277:30738–30745;2002.
  11. Mrowka R. A Java applet for visualizing protein-protein interaction. Bioinformatics 17:669–671;2001.
  12. Mukhopadhyay S, Mostafa J, Palakal M, Lam W, Xue L, Hudli A. An Adaptive Multi-level Information Filtering System. Proceedings of the Fifth International Conference on User Modeling, 21–28;1996.
  13. Palakal M, Mukhopadhyay S, Mostafa J, Raje R, N’Cho M, Mishra S. An intelligent biological information management system. Bioinformatics 18:1283–1288;2002.
  14. Pink JJ, Wuerzberger-Davis S, Tagliarino C, Planchon SM, Yang X, Froelich CJ, Boothman DA. Activation of a cysteine protease in MCF-7 and T47D breast cancer cells during beta-lapachone-mediated apoptosis. Exp Cell Res 255:144–155;2000.
  15. Pratt W, Yetisgen-Yildiz M. LitLinker: capturing connections across the biomedical literature. Proceedings of the International Conference on Knowledge Capture 105–112;2003.
  16. Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards: encyclopedia for genes, proteins and diseases. Weizmann Institute of Science, Bioinformatics Unit and Genome Center (Rehovot, Israel) 1997.
  17. Salton G. Automatic Text Processing: The Transformation, Analysis, and Retrieval of Information by Computer. Reading, Addison-Wesley, 1989.
  18. Stapley BJ, Benoit G. Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac Symp Biocomput 5:529–540;2000.
  19. Stephens M, Palakal M, Mukhopadhyay S, Raje R, Mostafa J. Detecting gene relations from Medline abstracts. Pac Symp Biocomput 483–495;2001.
  20. Sun Microsystems, Inc. demonstration software. Santa Clara, Sun Microsystems, 1995.
  21. Swanson DR. Fish oil, Raynaud’s syndrome, and undiscovered public knowledge. Perspect Biol Med 30:7–18;1986.
  22. Swanson DR. Migraine and magnesium: eleven neglected connections. Perspect Biol Med 31:526–557;1988.
  23. Swanson DR, Smalheiser NR. An interactive system for finding complementary literatures: a stimulus to scientific discovery. Artif Intell 91:183–203;1997.
  24. Tagliarino C, Pink JJ, Dubyak GR, Nieminen AL, Boothman DA. Calcium is a key signaling molecule in beta-lapachone-mediated cell death. J Biol Chem 276:19150–19159;2001.
  25. Tagliarino C, Pink JJ, Reinicke KE, Simmers SM, Wuerzberger-Davis SM, Boothman DA. Mu-calpain activation in beta-lapachone-mediated apoptosis. Cancer Biol Ther 2:141–152;2003.
  26. Warshall S. A theorem on boolean matrices. J ACM 9:11–12;1962.
  27. Wong PK, Whitney P, Thomas J. Visualizing Association Rules for Text Mining. Proceedings of IEEE Information Visualization, 120–123;1999.
  28. Wu WJ, Tu S, Cerione RA. Activated Cdc42 sequesters c-Cbl and prevents EGF receptor degradation. Cell 114:715–725;2003.

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