Building the process-drug-side effect network to discover the relationship between biological Processes and side effects

BMC Bioinformatics

Volumn 12, Issue SUPPL. 2, 2011, Pages

  Lee, Sejoon ^a   Lee, Kwang H ^a   Song, Min ^b   Lee, Doheon ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b NEW JERSEY INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; GENE ONTOLOGY; HUMAN BODIES; MULTI-LEVEL NETWORKS; PROCESS NETWORKS; RESPONSE PROCESS; SYSTEMATIC STUDY; TEXT-MINING;

DRUG THERAPY; MERGING;

DRUG INTERACTIONS;

DRUG;

ARTICLE; BIOLOGY; DATA BASE; DATA MINING; DRUG SURVEILLANCE PROGRAM; HUMAN; METHODOLOGY; PHENOTYPE;

ADVERSE DRUG REACTION REPORTING SYSTEMS; COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES AS TOPIC; HUMANS; PHARMACEUTICAL PREPARATIONS; PHENOTYPE;

EID: 79953072390     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S1-S2     Document Type: Article

References (26)

1. Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science 2008, 321(5886):263-266. New York, NY, 10.1126/science.1158140, 18621671.
2. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, et al. Predicting new molecular targets for known drugs. Nature 2009, 462(7270):175-181. 10.1038/nature08506, 2784146, 19881490.
3. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP, Subramanian A, Ross KN, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006, 313(5795):1929-1935. New York, NY, 10.1126/science.1132939, 17008526.
4. Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capture phenotypic effects of drugs. Molecular systems biology 6:343. 2824526, 20087340.
5. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
6. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(43):15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
7. Wu B. Cancer outlier differential gene expression detection. Biostatistics 2007, 8(3):566-575. 10.1093/biostatistics/kxl029, 17021278.
8. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 2008, 34:D901-6.
9. Lafferty J, McCallum A, Pereira F. Condition random fields: probabilistic models for segmenting and labeling sequence data. Proc. 18th International conf. on Machine Learning 282-289.
10. Brill E. A simple rule-based part of speech tagger. HLT'91 Proceeding of the workshop on speech and Natural Language 1992, 112-116.
11. Phan X. CRFChunker: CRF English Phrase Chunker. 2006, http://crfchunker.sourceforge.net/
12. Rudniy A, Song M, Geller J. Detecting Duplicate Biological Entities Using Path Edit Distance. International Journal of Data Mining and Bioinformatics 2010,
13. Hodges LC, Cook JD, Lobenhofer EK, Li L, Bennett L, Bushel PR, Aldaz CM, Afshari CA, Walker CL. Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells. Mol Cancer Res 2003, 1(4):300-311.
14. Neeman M, Degani H. Metabolic studies of estrogen- and tamoxifen-treated human breast cancer cells by nuclear magnetic resonance spectroscopy. Cancer research 1989, 49(3):589-594.
15. Suarez Y, Fernandez C, Gomez-Coronado D, Ferruelo AJ, Davalos A, Martinez-Botas J, Lasuncion MA. Synergistic upregulation of low-density lipoprotein receptor activity by tamoxifen and lovastatin. Cardiovascular research 2004, 64(2):346-355. 10.1016/j.cardiores.2004.06.024, 15485695.
16. Byun HO, Han NK, Lee HJ, Kim KB, Ko YG, Yoon G, Lee YS, Hong SI, Lee JS. Cathepsin D and eukaryotic translation elongation factor 1 as promising markers of cellular senescence. Cancer research 2009, 69(11):4638-4647. 10.1158/0008-5472.CAN-08-4042, 19487283.
17. Kesterson RA, Berbari NF, Pasek RC, Yoder BK. Utilization of conditional alleles to study the role of the primary cilium in obesity. Methods in cell biology 2009, 94:163-179. full_text, 20362090.
18. Rosner IA, Malemud CJ, Hassid AI, Goldberg VM, Boja BA, Moskowitz RW. Estradiol and tamoxifen stimulation of lapine articular chondrocyte prostaglandin synthesis. Prostaglandins 1983, 26(1):123-138. 10.1016/0090-6980(83)90080-1, 6635209.
19. Lahoute C, Sotiropoulos A, Favier M, Guillet-Deniau I, Charvet C, Ferry A, Butler-Browne G, Metzger D, Tuil D, Daegelen D. Premature aging in skeletal muscle lacking serum response factor. PloS one 2008, 3(12):e3910. 10.1371/journal.pone.0003910, 2593784, 19079548.
20. Yoneyama Y, Sawa R, Suzuki S, Otsubo Y, Araki T. Serum adenosine deaminase activity in women with hyperemesis gravidarum. Clinica chimica acta; international journal of clinical chemistry 2002, 324(1-2):141-145. 10.1016/S0009-8981(02)00236-X, 12204436.
21. Wang CZ, Fishbein A, Aung HH, Mehendale SR, Chang WT, Xie JT, Li J, Yuan CS. Polyphenol contents in grape-seed extracts correlate with antipica effects in cisplatin-treated rats. Journal of alternative and complementary medicine 2005, 11(6):1059-1065. New York, NY.
22. Ezrin C, Salter JM, Ogryzlo MA, Best CH. The Clinical and Metabolic Effects of Glucagon. Can Med Assoc J 1957, 78(2):3.
23. Kronfol Z, Remick DG. Cytokines and the brain: implications for clinical psychiatry. The American journal of psychiatry 2000, 157(5):683-694. 10.1176/appi.ajp.157.5.683, 10784457.
24. Hesketh PJ. Chemotherapy-induced nausea and vomiting. The New England journal of medicine 2008, 358(23):2482-2494. 10.1056/NEJMra0706547, 18525044.
25. Levina AA, Andreeva AP, Tsvetaeva NV, Tsibul'skaia MM, Minaeva LM, Tokarev Iu N. [Antioxidant activity of blood serum amd erythrocytes in patients with refractory anemia]. Gematologiia i transfuziologiia 1991, 36(7):11-14.
26. Morceau F, Dicato M, Diederich M. Pro-inflammatory cytokine-mediated anemia: regarding molecular mechanisms of erythropoiesis. Mediators of inflammation 2009, 2009:405016. 10.1155/2009/405016, 2830572, 20204172.