The UMD-p53 database: new mutations and analysis tools - PubMed (original) (raw)
Review
The UMD-p53 database: new mutations and analysis tools
Christophe Béroud et al. Hum Mutat. 2003 Mar.
Abstract
The tumor suppressor gene TP53 (p53) is the most extensively studied gene involved in human cancers. More than 1,400 publications have reported mutations of this gene in 150 cancer types for a total of 14,971 mutations. To exploit this huge bulk of data, specific analytic tools were highly warranted. We therefore developed a locus-specific database software called UMD-p53. This database compiles all somatic and germline mutations as well as polymorphisms of the TP53 gene which have been reported in the published literature since 1989, or unpublished data submitted to the database curators. The database is available at www.umd.necker.fr or at http://p53.curie.fr/. In this paper, we describe recent developments of the UMD-p53 database. These developments include new fields and routines. For example, the analysis of putative acceptor or donor splice sites is now automated and gives new insight for the causal role of "silent mutations." Other routines have also been created such as the prescreening module, the UV module, and the cancer distribution module. These new improvements will help users not only for molecular epidemiology and pharmacogenetic studies but also for patient-based studies. To achieve theses purposes we have designed a procedure to check and validate data in order to reach the highest quality data.
Copyright 2003 Wiley-Liss, Inc.
Similar articles
- The UMD TP53 database and website: update and revisions.
Hamroun D, Kato S, Ishioka C, Claustres M, Béroud C, Soussi T. Hamroun D, et al. Hum Mutat. 2006 Jan;27(1):14-20. doi: 10.1002/humu.20269. Hum Mutat. 2006. PMID: 16278824 - The IARC TP53 database: new online mutation analysis and recommendations to users.
Olivier M, Eeles R, Hollstein M, Khan MA, Harris CC, Hainaut P. Olivier M, et al. Hum Mutat. 2002 Jun;19(6):607-14. doi: 10.1002/humu.10081. Hum Mutat. 2002. PMID: 12007217 - UMD (Universal Mutation Database): 2005 update.
Béroud C, Hamroun D, Collod-Béroud G, Boileau C, Soussi T, Claustres M. Béroud C, et al. Hum Mutat. 2005 Sep;26(3):184-91. doi: 10.1002/humu.20210. Hum Mutat. 2005. PMID: 16086365 - The UMD-LDLR database: additions to the software and 490 new entries to the database.
Villéger L, Abifadel M, Allard D, Rabès JP, Thiart R, Kotze MJ, Béroud C, Junien C, Boileau C, Varret M. Villéger L, et al. Hum Mutat. 2002 Aug;20(2):81-7. doi: 10.1002/humu.10102. Hum Mutat. 2002. PMID: 12124988 Review. - IARC p53 mutation database: a relational database to compile and analyze p53 mutations in human tumors and cell lines. International Agency for Research on Cancer.
Hernandez-Boussard T, Rodriguez-Tome P, Montesano R, Hainaut P. Hernandez-Boussard T, et al. Hum Mutat. 1999;14(1):1-8. doi: 10.1002/(SICI)1098-1004(1999)14:1<1::AID-HUMU1>3.0.CO;2-H. Hum Mutat. 1999. PMID: 10447253 Review.
Cited by
- Crocetin exploits p53-induced death domain (PIDD) and FAS-associated death domain (FADD) proteins to induce apoptosis in colorectal cancer.
Ray P, Guha D, Chakraborty J, Banerjee S, Adhikary A, Chakraborty S, Das T, Sa G. Ray P, et al. Sci Rep. 2016 Sep 13;6:32979. doi: 10.1038/srep32979. Sci Rep. 2016. PMID: 27622714 Free PMC article. - At a glance: A history of autophagy and cancer.
Wen X, Klionsky DJ. Wen X, et al. Semin Cancer Biol. 2020 Nov;66:3-11. doi: 10.1016/j.semcancer.2019.11.005. Epub 2019 Nov 7. Semin Cancer Biol. 2020. PMID: 31707087 Free PMC article. Review. - A global suppressor motif for p53 cancer mutants.
Baroni TE, Wang T, Qian H, Dearth LR, Truong LN, Zeng J, Denes AE, Chen SW, Brachmann RK. Baroni TE, et al. Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):4930-5. doi: 10.1073/pnas.0401162101. Epub 2004 Mar 22. Proc Natl Acad Sci U S A. 2004. PMID: 15037740 Free PMC article. - High sensitivity EndoV mutation scanning through real-time ligase proofreading.
Pincas H, Pingle MR, Huang J, Lao K, Paty PB, Friedman AM, Barany F. Pincas H, et al. Nucleic Acids Res. 2004 Oct 28;32(19):e148. doi: 10.1093/nar/gnh150. Nucleic Acids Res. 2004. PMID: 15514109 Free PMC article. - tp53 mutant zebrafish develop malignant peripheral nerve sheath tumors.
Berghmans S, Murphey RD, Wienholds E, Neuberg D, Kutok JL, Fletcher CD, Morris JP, Liu TX, Schulte-Merker S, Kanki JP, Plasterk R, Zon LI, Look AT. Berghmans S, et al. Proc Natl Acad Sci U S A. 2005 Jan 11;102(2):407-12. doi: 10.1073/pnas.0406252102. Epub 2005 Jan 3. Proc Natl Acad Sci U S A. 2005. PMID: 15630097 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials
Miscellaneous