CMPD: Cancer mutant proteome database

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D849-D855

  Huang, Po Jung ^a   Lee, Chi Ching ^a   Tan, Bertrand Chin Ming ^a   Yeh, Yuan Ming ^b   Chu, Lichieh Julie ^a   Chen, Ting Wen ^a   Chang, Kai Ping ^c   Lee, Cheng Yang ^a   Gan, Ruei Chi ^a   Liu, Hsuan ^a   Tang, Petrus ^a  

^a CHANG GUNG UNIVERSITY   (Taiwan)

^b Bioinformatics Division   (Taiwan)

^c CHANG GUNG MEMORIAL HOSPITAL   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER MUTANT PROTEOME DATABASE; CANCER RESEARCH; EXOME; FACTUAL DATABASE; GENE MUTATION; GENETIC ASSOCIATION; GENETIC VARIABILITY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; PROTEOMICS; SEQUENCE ANALYSIS; TRANSLATIONAL RESEARCH; GENETICS; HUMAN; INTERNET; MUTATION; NEOPLASM; PROTEIN DATABASE; TUMOR CELL LINE;

MUTANT PROTEIN; PROTEOME; TUMOR PROTEIN;

CELL LINE, TUMOR; DATABASES, PROTEIN; HUMANS; INTERNET; MUTANT PROTEINS; MUTATION; NEOPLASM PROTEINS; NEOPLASMS; PROTEOME;

EID: 84946093959     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1182     Document Type: Article

References (36)

1. Kandoth, C., McLellan, M. D., Vandin, F., Ye, K., Niu, B., Lu, C., Xie, M., Zhang, Q., McMichael, J. F., Wyczalkowski, M. A. et al. (2013) Mutational landscape and significance across 12 major cancer types. Nature, 502, 333-339.
2. Abaan, O. D., Polley, E. C., Davis, S. R., Zhu, Y. J., Bilke, S., Walker, R. L., Pineda, M., Gindin, Y., Jiang, Y., Reinhold, W. C. et al. (2013) The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. Cancer Res., 73, 4372-4382.
3. Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D. et al. (2012) The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature, 483, 603-607.
4. Gholami, A. M., Hahne, H., Wu, Z., Auer, F. J., Meng, C., Wilhelm, M. and Kuster, B. (2013) Global proteome analysis of the NCI-60 cell line panel. Cell Rep., 4, 609-620.
5. Fournier, F., Joly Beauparlant, C, Paradis, R. and Droit, A. (2014) rTANDEM, an R/Bioconductor package for MS/MS protein identification. Bioinformatics, 30, 2233-2234.
6. Tabb, D. L., Fernando, C. G. and Chambers, M. C. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res., 6, 654-661.
7. Yang, X. and Lazar, I. M. (2014) XMAn: a Homo sapiens mutated-peptide database for the MS analysis of cancerous cell states. J. Proteome Res., doi:10.1021/pr5004467.
8. Forbes, S. A., Bindal, N., Bamford, S. and Cole, C. (2010) COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res., 39, D945-D950.
9. Petitjean, A., Mathe, E., Kato, S., Ishioka, C, Tavtigian, S. V, Hainaut, P. and Olivier, M. (2007) Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. Hum. Mutat., 28, 622-629.
10. Amberger, J., Bocchini, C and Hamosh, A. (2011) A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Hum. Mutat., 32, 564-567.
11. Consortium, U. (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
12. Mathivanan, S., Ji, H., Tauro, B. J. and Chen, Y. S. (2012) Identifying mutated proteins secreted by colon cancer cell lines using mass spectrometry. J. Proteomics, 76, 141-149.
13. Li, J., Duncan, D. T. and Zhang, B. (2010) CanProVar: a human cancer proteome variation database. Hum. Mutat., 31, 219-228.
14. Sherry, S. T. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
15. Koboldt, D. C, Fulton, R. S., McLellan, M. D., Schmidt, H., Kalicki-Veizer, J., McMichael, J. F, Fulton, L. L., Dooling, D. J., Ding, L., Mardis, E. R. et al. (2012) Comprehensive molecular portraits of human breast tumours. Nature, 490, 61-70.
16. Muzny, D. M., Muzny, D. M., Bainbridge, M. N., Bainbridge, M. N., Chang, K., Chang, K., Dinh, H. H., Dinh, H. H., Drummond, J. A., Drummond, J. A. et al. (2012). Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487, 330-337.
17. Cancer Genome Atlas Research Network (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature, 489, 519-525.
18. Liu, X., Jian, X. and Boerwinkle, E. (2013) dbNSFP v2. 0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum. Mutat., 34, 2393-2402.
19. Landrum, M. J., Lee, J. M., Riley, G. R., Jang, W., Rubinstein, W. S., Church, D. M. and Maglott, D. R. (2013) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res., 42, D980-D985.
20. Perkins, D. N., Pappin, D. J., Creasy, D. M. and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20, 3551-3567.
21. Eng, J. K., McCormack, A. L. and Yates, J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom., 5, 976-989.
22. Flicek, P, Amode, M. R., Barrell, D. and Beal, K. (2013) Ensembl 2014. Nucleic Acids Res., 42, D749-D755.
23. Kasprzyk, A. (2011) BioMart: driving a paradigm change in biological data management. Database (Oxford), 2011, bar049.
24. Mangan, M. E., Williams, J. M., Kuhn, R. M. and Lathe, W. C (2014) The UCSC genome browser: what every molecular biologist should know. Curr Protoc. Mol. Biol, 107, 19.9.1-19.9.36.
25. Gray, K. A., Daugherty, L. C, Gordon, S. M., Seal, R. L., Wright, M. W and Bruford, E. A. (2013) Genenames.org: the HGNC resources in 2013. Nucleic Acids Res., 41, D545-D552.
26. Pruitt, K. D., Brown, GR., Hiatt, S. M., Thibaud-Nissen, F, Astashyn, A., Ermolaeva, O., Farrell, CM., Hart, J., Landrum, M. J., McGarvey, K. M. et al. (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res., 42, D756-D763.
27. The Gene Ontology Consortium (2009) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res., 38, D331-D335.
28. Kanehisa, M., Goto, S., Sato, Y. and Furumichi, M. (2011) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
29. Wang, K., Li, M. and Hakonarson, H. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res., 38, e164.
30. - 1000 Genomes Project Consortium, Abecasis, G. R., Auton, A., Brooks, L. D., DePristo, M. A., Durbin, R. M., Handsaker, R. E., Kang, H. M., Marth, G. T. and McVean, G. A. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
31. Fu, W., O'Connor, T. D., Jun, G., Kang, H. M., Abecasis, G., Leal, S. M., Gabriel, S., Rieder, M. J., Altshuler, D., Shendure, J. et al. (2013) Analysis of 6, 515 exomes reveals the recent origin of most human protein-coding variants. Nature, 493, 216-220.
32. Sim, N. L., Kumar, P., Hu, J., Henikoff, S., Schneider, G. and Ng, P. C. (2012) SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res., 40, W452-W457.
33. Schwarz, J. M., Rödelsperger, C., Schuelke, M. and Seelow, D. (2010) MutationTaster evaluates disease-causing potential of sequence alterations. Nat. Methods, 7, 575-576.
34. Chun, S. and Fay, J. C. (2009) Identification of deleterious mutations within three human genomes. Genome Res., 19, 1553-1561.
35. Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S. and Sunyaev, S. R. (2010) A method and server for predicting damaging missense mutations. Nat. Methods, 7, 248-249.
36. Wang, X., Slebos, R. J. C., Wang, D., Halvey, P. J., Tabb, D. L., Liebler, D. C. and Zhang, B. (2012) Protein identification using customized protein sequence databases derived from RNA-Seq data. J. Proteome Res., 11, 1009-1017.