CancerResource: A comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Ahmed, Jessica ^a   Meinel, Thomas ^a   Dunkel, Mathias ^a   Murgueitio, Manuela S ^a   Adams, Robert ^a   Blasse, Corinna ^a   Eckert, Andreas ^a   Preissner, Saskia ^a   Preissner, Robert ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER RESEARCH; CANCERRESOURCE DATABASE; CELL GROWTH; CONTROLLED STUDY; DATA MINING; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE INTERACTION; HUMAN; HUMAN CELL; INFORMATION PROCESSING; PHARMACOGENOMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION;

ANTINEOPLASTIC AGENTS; CELL LINE, TUMOR; DATA MINING; DATABASES, PROTEIN; GENE EXPRESSION; HUMANS; NEOPLASM PROTEINS; SOFTWARE; SYSTEMS INTEGRATION;

EID: 78651324797     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq910     Document Type: Article

References (36)

1. Wishart,D.S.(2007) Discovering drug targets through the web. Comp. Biochem. Physiol. Part D Genomics Proteomics, 2, 9-17.
2. Meinel,T. and Herwig,R.(2010) SOAP/WSDL-based Web Services for Biomedicine. In Lazakidou,A.(ed.), Web-Based Applications in Healthcare and Biomedicine. Springer, New York, USA, pp. 101-116.
3. Amberger,J., Bocchini,C.A., Scott,A.F. and Hamosh,A.(2009) McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res., 37, D793-796.
4. Forbes,S.A., Tang,G., Bindal,N., Bamford,S., Dawson,E., Cole,C., Kok,C.Y., Jia,M., Ewing,R., Menzies,A.et al. (2010) COSMIC (the Catalogue of Somatic Mutations in Cancer): A resource to investigate acquired mutations in human cancer. Nucleic Acids Res., 38, D652-D657.
5. Hanahan,D. and Weinberg,R.A.(2000) The hallmarks of cancer. Cell, 100, 57-70.
6. Hopkins,A.L. and Groom,C.R.(2002) The druggable genome. Nat. Rev. Drug Discov., 1, 727-730.
7. Sophic Alliance. (2010) The Integrated Druggable Genome Database. Sophic Systems Alliance Inc, Rockville, MD, USA.
8. Davis,A.P., Murphy,C.G., Saraceni-Richards,C.A., Rosenstein,M.C., Wiegers,T.C. and Mattingly,C.J.(2009) Comparative Toxicogenomics Database: A knowledgebase and discovery tool for chemical-gene-disease networks. Nucleic Acids Res., 37, D786-D792.
9. Hernandez-Boussard,T., Whirl-Carrillo,M., Hebert,J.M., Gong,L., Owen,R., Gong,M., Gor,W., Liu,F., Truong,C., Whaley,R. et al. (2008) The pharmacogenetics and pharmacogenomics knowledge base: Accentuating the knowledge. Nucleic Acids Res., 36, D913-D918.
10. Zhu,F., Han,B., Kumar,P., Liu,X., Ma,X., Wei,X., Huang,L., Guo,Y., Han,L., Zheng,C. et al. (2010) Update of TTD: Therapeutic Target Database. Nucleic Acids Res., 38, D787-D791.
11. Wishart,D.S., Knox,C., Guo,A.C., Cheng,D., Shrivastava,S., Tzur,D., Gautam,B. and Hassanali,M.(2008) DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res., 36, D901-D906.
12. Shoemaker,R.H.(2006) The NCI60 human tumour cell line anticancer drug screen. Nat. Rev. Cancer, 6, 813-823.
13. Mattingly,C.J.(2009) Chemical databases for environmental health and clinical research. Toxicol. Lett., 186, 62-65.
14. McEntyre,J. and Lipman,D.(2001) PubMed: Bridging the information gap. Can. Med. Assoc. J., 164, 1317-1319.
15. Goede,A., Dunkel,M., Mester,N., Frommel,C. and Preissner,R.(2005) SuperDrug: A conformational drug database. Bioinformatics, 21, 1751-1753.
16. 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. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
17. McCandless,M., Hatcher,E. and Gospodnetić,O.(2010) Lucene in Action, 2nd edn. Manning Publications Co, Greenwich, CT, USA.
18. Berman,H., Henrick,K., Nakamura,H. and Markley,J.L.(2007) The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
19. Wang,Y., Bolton,E., Dracheva,S., Karapetyan,K., Shoemaker,B.A., Suzek,T.O., Wang,J., Xiao,J., Zhang,J. and Bryant,S.H.(2010) An overview of the PubChem BioAssay resource. Nucleic Acids Res., 38, D255-D266.
20. Gunther,S., Kuhn,M., Dunkel,M., Campillos,M., Senger,C., Petsalaki,E., Ahmed,J., Urdiales,E.G., Gewiess,A., Jensen,L.J. et al. (2008) SuperTarget and Matador: Resources for exploring drug-target relationships. Nucleic Acids Res., 36, D919-D922.
21. UniProtConsortium. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
22. Flicek,P., Aken,B.L., Ballester,B., Beal,K., Bragin,E., Brent,S., Chen,Y., Clapham,P., Coates,G., Fairley,S. et al. (2010) Ensembl's 10th year. Nucleic Acids Res., 38, D557-D562.
23. Kamburov,A., Wierling,C., Lehrach,H. and Herwig,R.(2009) ConsensusPathDB: A database for integrating human functional interaction networks. Nucleic Acids Res., 37, D623-D628.
24. Ruepp,A., Brauner,B., Dunger-Kaltenbach,I., Frishman,G., Montrone,C., Stransky,M., Waegele,B., Schmidt,T., Doudieu,O.N., Stumpflen,V. et al. (2008) CORUM: The comprehensive resource of mammalian protein complexes. Nucleic Acids Res., 36, D646-D650.
25. Hoffmann,R. and Valencia,A.(2004) A gene network for navigating the literature. Nat. Genet., 36, 664.
26. Matthews,L., Gopinath,G., Gillespie,M., Caudy,M., Croft,D., de Bono,B., Garapati,P., Hemish,J., Hermjakob,H., Jassal,B. et al. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res., 37, D619-D622.
27. Meinel,T., Krause,A., Luz,H., Vingron,M. and Staub,E.(2005) The SYSTERS Protein Family Database in 2005. Nucleic Acids Res., 33, D226-D229.
28. Finn,R.D., Mistry,J., Tate,J., Coggill,P., Heger,A., Pollington,J.E., Gavin,O.L., Gunasekaran,P., Ceric,G., Forslund,K. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
29. Kanehisa,M., Goto,S., Hattori,M., Aoki-Kinoshita,K.F., Itoh,M., Kawashima,S., Katayama,T., Araki,M. and Hirakawa,M.(2006) From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res., 34, D354-D357.
30. Fullbeck,M., Dunkel,M., Hossbach,J., Daniel,P.T. and Preissner,R.(2009) Cellular fingerprints: A novel approach using large-scale cancer cell line data for the identification of potential anticancer agents. Chem. Biol. Drug Des., 74, 439-448.
31. Lamb,J., Crawford,E.D., Peck,D., Modell,J.W., Blat,I.C., Wrobel,M.J., Lerner,J., Brunet,J.P., Subramanian,A., Ross,K.N. et al. (2006) The Connectivity Map: Using gene-expression signatures to connect small molecules, genes, and disease. Science, 313, 1929-1935.
32. Edgar,R., Domrachev,M. and Lash,A.E.(2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
33. Hewelt,A., Ben Kahla,A., Hennig,S., Nagel,A., Himmelbauer,H., Zehetner,G., Haas,S., Vingron,M., Yaspo,M.L. and Lehrach,H.(2002) Human Genome Meeting HGM2002. Shanghai, China, Abstract 23.
34. Meinel,T., Mueller,M.S., Ahmed,J., Yildirimman,R., Dunkel,M., Herwig,R. and Preissner,R.(2010) SOAP/WSDL-based web services for biomedicine: Demonstrating the technique with the CancerResource. In Bamidis,P.D. and Pallikarakis,N.(eds), XII Mediterranean Conference on Medical and Biological Engineering and Computing 2010. Springer, Berlin Heidelberg, Chalkidiki, Greece, pp. 835-838.
35. Thimm,M., Goede,A., Hougardy,S. and Preissner,R.(2004) Comparison of 2D similarity and 3D superposition. Application to searching a conformational drug database. J. Chem. Inf. Comput. Sci., 44, 1816-1822.
36. Masseroli,M. and Tagliasacchi,M.(2010) Web resources for gene list analysis in biomedicine. In Lazakidou,A.(ed.), Web-Based Applications in Healthcare and Biomedicine. Springer, New York, USA, pp. 117-141.