dbDEPC: A database of differentially expressed proteins in human cancers

Nucleic Acids Research

Volumn 38, Issue SUPPL.1, 2009, Pages

  Li, Hong ^a,b   He, Ying ^a,b   Ding, Guohui ^a   Wang, Chuan ^a   Xie, Lu ^b   Li, Yixue ^a,b  

^a Chinese Academy of Sciences   (China)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEOME; RNA;

AMINO ACID SEQUENCE; ARTICLE; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; HUMAN; INFORMATION RETRIEVAL; MALIGNANT NEOPLASTIC DISEASE; MASS SPECTROMETRY; MEDICAL RESEARCH; PEER REVIEW; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN STRUCTURE; PROTEOMICS; PUBLICATION; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS; BIOLOGY; COMPUTER PROGRAM; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HUMAN GENOME; INTERNET; METABOLISM; METHODOLOGY; NEOPLASM;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; DNA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; NEOPLASMS; PROTEOME; RNA; SOFTWARE;

EID: 75549084371     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp933     Document Type: Article

References (24)

1. Hanahan, D. and Weinberg, R.A. (2000) The hallmarks of cancer. Cell, 100, 57-70.
2. Ross, D.T., Scherf, U., Eisen, M.B., Perou, C.M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S.S., Van de Rijn, M., Waltham, M. et al. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet., 24, 227-235.
3. Kato, K., Yamashita, R., Matoba, R., Monden, M., Noguchi, S., Takagi, T. and Nakai, K. (2005) Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res., 33, D533-536.
4. Elfilali, A., Lair, S., Verbeke, C., La Rosa, P., Radvanyi, F. and Barillot, E. (2006) ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. Nucleic Acids Res., 34, D613-616.
5. Forbes, S.A., Bhamra, G., Bamford, S., Dawson, E., Kok, C., Clements, J., Menzies, A., Teague, J.W., Futreal, P.A. and Stratton, M.R. (2008) The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr. Protoc. Hum. Genet., Chapter 10, Unit 10 11.
6. Semmes, O.J., Malik, G. and Ward, M. (2006) Application of mass spectrometry to the discovery of biomarkers for detection of prostate cancer. J. Cell Biochem., 98, 496-503.
7. Ong, S.E., Foster, L.J. and Mann, M. (2003) Mass spectrometric-based approaches in quantitative proteomics. Methods, 29, 124-130.
8. Pan, J., Chen, H.Q., Sun, Y.H., Zhang, J.H. and Luo, X.Y. (2008) Comparative proteomic analysis of non-small-cell lung cancer and normal controls using serum label-free quantitative shotgun technology. Lung, 186, 255-261.
9. Ueda, K., Katagiri, T., Shimada, T., Irie, S., Sato, T.A., Nakamura, Y. and Daigo, Y. (2007) Comparative profiling of serum glycoproteome by sequential purification of glycoproteins and 2-nitrobenzensulfenyl (NBS) stable isotope labeling: a new approach for the novel biomarker discovery for cancer. J. Proteome Res., 6, 3475-3483.
10. Chen, G., Li, A., Zhao, M., Gao, Y., Zhou, T., Xu, Y., Du, Z., Zhang, X. and Yu, X. (2008) Proteomic analysis identifies protein targets responsible for depsipeptide sensitivity in tumor cells. J. Proteome Res., 7, 2733-2742.
11. Bouchal, P., Roumeliotis, T., Hrstka, R., Nenutil, R., Vojtesek, B. and Garbis, S.D. (2009) Biomarker discovery in low-grade breast cancer using isobaric stable isotope tags and two-dimensional liquid chromatography-tandem mass spectrometry (iTRAQ-2DLC-MS/MS) based quantitative proteomic analysis. J. Proteome Res., 8, 362-373.
12. Deng, S.S., Xing, T.Y., Zhou, H.Y., Xiong, R.H., Lu, Y.G., Wen, B., Liu, S.Q. and Yang, H.J. (2006) Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human. Gen. Proteom. Bioinfo., 4, 165-172.
13. Ho, J., Kong, J.W., Choong, L.Y., Loh, M.C., Toy, W., Chong, P.K., Wong, C.H., Wong, C.Y., Shah, N. and Lim, Y.P. (2009) Novel breast cancer metastasis-associated proteins. J. Proteome Res., 8, 583-594.
14. Yocum, A.K., Busch, C.M., Felix, C.A. and Blair, I.A. (2006) Proteomics-based strategy to identify biomarkers and pharmacological targets in leukemias with t(4;11) translocations. J. Proteome Res., 5, 2743-2753.
15. Ralhan, R., Desouza, L.V., Matta, A., Chandra Tripathi, S., Ghanny, S., Dattagupta, S., Thakar, A., Chauhan, S.S. and Siu, K.W. (2009) iTRAQ-multidimensional liquid chromatography and tandem mass spectrometry-based identification of potential biomarkers of oral epithelial dysplasia and novel networks between inflammation and premalignancy. J. Proteome Res., 8, 300-309.
16. Kersey, P.J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E. and Apweiler, R. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics, 4, 1985-1988.
17. Altschul, S.F., Madden, T.L., Schaffer, 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, 3389-3402.
18. Li, H., Ding, G., Xie, L. and Li, Y. (2009) PAnnBuilder: an R package for assembling proteomic annotation data. Bioinformatics, 25, 1094-1095.
19. 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.
20. Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.R., Ceric, G., Forslund, K., Eddy, S.R., Sonnhammer, E.L. et al. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-288.
21. Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
22. Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M. and Sirotkin, K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
23. Zhang, J., Feuk, L., Duggan, G.E., Khaja, R. and Scherer, S.W. (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet. Genome Res., 115, 205-214.
24. Frese, K.K. and Tuveson, D.A. (2007) Maximizing mouse cancer models. Nat. Rev. Cancer, 7, 645-658.