a table listing the peptides recognized by T cells extracted from the database at http://www.cancerimmun ity.org/peptidedatabase/tumorspeciﬁc.htm. The ‘Induced immune response’ section lists the results, with links to PubMed, from published clinical trials in which cancer patients received CT antigen-based vaccines. Finally, the tab ‘PubMed’ hosts all the references related to individual gene entries. IMPLEMENTATION CTdatabase runs on free software (MySQL database server, Apache WWW server with the interface written in PHP). Perl and shell scripts were written to parse down- loaded data. FUTURE DIRECTIONS Most of the work done on CT antigens has focused on the immunologic aspects of this intriguing family of proteins. However, a central question that remains to be answered is whether CT antigen expression contributes to tumori- genesis or is a functionally irrelevant by-product of the process of cellular transformation. Initial structural and functional information on CT antigens indicate that CT antigen expression could have a fundamental role in human tumorigenesis. Knowledge on diﬀerent aspects of CT antigens is continuously expanding and we plan to update the CTdatabase structure by adding new infor- mation as it appears in the literature. In addition, the high-throughput data will also be upgraded periodically. FUNDING Conselho Nacional de Desenvolvimento Cientı´ ﬁco e Tecnolo´ gico; Coordenac¸ a˜ o de Aperfeic¸ oamento de Pessoal de N ı´vel Superior; Fundac¸ a˜ o Carlos Chagas Filho de Amparo a` Pesquisa do Estado do Rio de Janeiro. Funding for open access charges: Ludwig Institute for Cancer Research. Conﬂict of interest statement. None declared. REFERENCES 1. Vansteenkiste,J.F., Zielinski,M., Dahabreh,I.J., Linder,A., Lehmann,F., Gruselle,O., Therasse,P., Louahed,J. and Nucleic Acids Research, 2009, Vol. 37, Database issue D819 Brichard,V.G. (2008) Association of gene expression signature and clinical eﬃcacy of MAGE-A3 antigenspeciﬁc cancer immunotherapeutic (ASCI) as adjuvant therapy in resected stage IB/II non-small cell lung cancer (NSCLC). J. Clin. Oncol., 26, 7501. 2. Davis,I.D., Chen,W., Jackson,H., Parente,P., Shackleton,M., Hopkins,W., Chen,Q., Dimopoulos,N., Luke,T., Murphy,R. et al. (2004) Recombinant NY-ESO-1 protein with ISCOMATRIX adjuvant induces broad integrated antibody and CD4(+) and CD8(+) T cell responses in humans. Proc. Natl Acad. Sci. USA, 101, 10697–10702. 3. van der Bruggen,P., Traversari,C., Chomez,P., Lurquin,C., De Plaen,E., Van den Eynde,B., Knuth,A. and Boon,T. (1991) A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma. Science, 254, 1643–1647. 4. Old,L.J. and Chen,Y.T. (1998) New paths in human cancer serol- ogy. J. Exp. Med., 187, 1163–1167. 5. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2007) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61–D65. 6. Wheeler,D.L., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., Dicuccio,M., Edgar,R., Federhen,S. et al. (2008) Database resources of the National Center for Biotechnology. Nucleic Acids Res., 36, D13–D21. 7. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2006) The human genome browser at UCSC. Genome Res., 12, 996–1006. 8. Altschul,S.F., Madden,T.L., Scha¨ ﬀer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI- BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–33402. 9. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position speciﬁc gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673–4680. 10. Kumar,S., Tamura,K. and Nei,M. (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform., 5, 150–163. 11. UniProt Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res., 36, D190–D195. 12. Velculescu,V.E., Zhang,L., Vogelstein,B. and Kinzler,K.W. (1995) Serial analysis of gene expression. Science, 270, 484–487. 13. Brenner,S., Johnson,M., Bridgham,J., Golda,G., Lloyd,D.H., Johnson,D., Luo,S., McCurdy,S., Foy,M., Ewan,M. et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol., 18, 630–634. 14. Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993) dbEST-database for ‘‘expressed sequence tags’’. Nat. Genet., 4, 332–333. 15. Boon,K., Osorio,E.C., Greenhut,S.F., Schaefer,C.F., Shoemaker,J., Polyak,K., Morin,P.J., Buetow,K.H., Strausberg,R.L., De Souza,S.J. et al. (2002) An anatomy of normal and malignant gene expression. Proc. Natl Acad. Sci. USA, 99, 11287–11292.