Nucleic Acids Research Advance Access originally published online on October 25, 2007
Nucleic Acids Research 2008 36(Database issue):D892-D900; doi:10.1093/nar/gkm755
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, Database issue D892-D900
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-com
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
CEBS—Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data
1NIEHS, National Center for Toxicogenomics, PO Box 12233, Research Triangle Park, NC 27709, 2Science Applications International Corporation, 1710 SAIC Drive, McLean, VA 22101, 3Large Scale Biology Corporation, 3333 Vaca Valley Parkway, Vacaville, CA 95688, 4Lockheed Martin Information Technologies, PO Box 12233, Research Triangle Park, North Carolina 27709, 5Research Triangle Institute, PO Box 12194, Research Triangle Park, NC 27709 and 6Alpha Gamma Technologies, Inc., 4700 Falls of Neuse Road, Suite 350, Raleigh, NC, 27609, USA
* To whom correspondence should be addressed. Tel: +1 919 541 5055; Email: fostel{at}niehs.nih.gov
Received June 28, 2007. Revised August 30, 2007. Accepted September 11, 2007.
CEBS (Chemical Effects in Biological Systems) is an integrated public repository for toxicogenomics data, including the study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. CEBS contains data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. CEBS is designed to permit the user to query the data using the study conditions, the subject responses and then, having identified an appropriate set of subjects, to move to the microarray module of CEBS to carry out gene signature and pathway analysis. Scope of CEBS: CEBS currently holds 22 studies of rats, four studies of mice and one study of Caenorhabditis elegans. CEBS can also accommodate data from studies of human subjects. Toxicogenomics studies currently in CEBS comprise over 4000 microarray hybridizations, and 75 2D gel images annotated with protein identification performed by MALDI and MS/MS. CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Additionally, clinical chemistry and histopathology findings from over 1500 animals are included in CEBS. CEBS/BID: The BID (Biomedical Investigation Database) is another component of the CEBS system. BID is a relational database used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee (in preparation). BID has been shared with Health Canada and the US Environmental Protection Agency. CEBS is available at http://cebs.niehs.nih.gov. BID can be accessed via the user interface from https://dir-apps.niehs.nih.gov/arc/. Requests for a copy of BID and for depositing data into CEBS or BID are available at http://www.niehs.nih.gov/cebs-df/.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. H. Harrill, P. K. Ross, D. M. Gatti, D. W. Threadgill, and I. Rusyn Population-Based Discovery of Toxicogenomics Biomarkers for Hepatotoxicity Using a Laboratory Strain Diversity Panel Toxicol. Sci., July 1, 2009; 110(1): 235 - 243. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. R. Williams-Devane, M. A. Wolf, and A. M. Richard Toward a Public Toxicogenomics Capability for Supporting Predictive Toxicology: Survey of Current Resources and Chemical Indexing of Experiments in GEO and ArrayExpress Toxicol. Sci., June 1, 2009; 109(2): 358 - 371. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. R. Williams-DeVane, M. A. Wolf, and A. M. Richard DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages Bioinformatics, March 1, 2009; 25(5): 692 - 694. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. P. Davis, C. G. Murphy, C. A. Saraceni-Richards, M. C. Rosenstein, T. C. Wiegers, and C. J. Mattingly Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks Nucleic Acids Res., January 1, 2009; 37(suppl_1): D786 - D792. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Schmidt, S. Struck, B. Gruening, J. Hossbach, I. S. Jaeger, R. Parol, U. Lindequist, E. Teuscher, and R. Preissner SuperToxic: a comprehensive database of toxic compounds Nucleic Acids Res., January 1, 2009; 37(suppl_1): D295 - D299. [Abstract] [Full Text] [PDF]
|
|