Skip Navigation



Bioinformatics Advance Access published online on January 22, 2004
Bioinformatics, doi:10.1093/bioinformatics/btg428
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
20/4/452    most recent
btg428v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Manduchi, E.
Right arrow Articles by Stoeckert, C. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Manduchi, E.
Right arrow Articles by Stoeckert, C. J., Jr.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received June 19, 2003
Revised August 9, 2003
Accepted August 11, 2003

Article

RAD and the RAD Study-Annotator: an approach to collection, organization, and exchange of all relevant information for high-throughput gene expression studies

E. Manduchi 1*, G. R. Grant 1, H. He 1, J. Liu 1, M. D. Mailman 1, A. D. Pizarro 1, P. L. Whetzel 1, C. J. Stoeckert Jr.1

1 Center for Bioinformatics, University of Pennsylvania, 14th floor Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104-6021, USA

* To whom correspondence should be addressed. E-mail: manduchi{at}pcbi.upenn.edu.


  Abstract

Motivation: Gene expression array technology has become increasingly widespread among researchers who recognize its numerous promises. At the same time, bench biologists and bioinformaticians have come to increasingly appreciate the importance of establishing a collaborative dialog from the onset of a study and of collecting and exchanging detailed information on the many experimental and computational procedures using a structured mechanism. This is crucial for adequate analyses of this kind of data.

Results: The RNA Abundance Database (RAD: http://www.cbil.upenn.edu/RAD) provides a comprehensive MIAME-supportive infrastructure for gene expression data management and makes extensive use of ontologies. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format (e.g. ArrayExpress). RAD is part of a more general Genomics Unified Schema (GUS: http://www.gusdb.org), which includes a richly annotated gene index (http://www.allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. This infrastructure enables a large variety of queries that incorporate visualization and analysis tools and have been tailored to serve the specific needs of projects focusing on particular organisms or biological systems.

Availability: The system is freely available. Information on how to obtain it and how to install it can be found at http://www.cbil.upenn.edu/RAD/RAD-installation.htm.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genes Dev.Home page
R. K. Gupta, N. Gao, R. K. Gorski, P. White, O. T. Hardy, K. Rafiq, J. E. Brestelli, G. Chen, C. J. Stoeckert Jr., and K. H. Kaestner
Expansion of adult beta-cell mass in response to increased metabolic demand is dependent on HNF-4{alpha}
Genes & Dev., April 1, 2007; 21(7): 756 - 769.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Endocrinol.Home page
O. T. Hardy, H. E. Hohmeier, T. C. Becker, E. Manduchi, N. M. Doliba, R. K. Gupta, P. White, C. J. Stoeckert Jr, F. M. Matschinsky, C. B. Newgard, et al.
Functional Genomics of the {beta}-Cell: Short-Chain 3-Hydroxyacyl-Coenzyme A Dehydrogenase Regulates Insulin Secretion Independent of K+ Currents
Mol. Endocrinol., March 1, 2007; 21(3): 765 - 773.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. M. Mazzarelli, J. Brestelli, R. K. Gorski, J. Liu, E. Manduchi, D. F. Pinney, J. Schug, P. White, K. H. Kaestner, and C. J. Stoeckert Jr
EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D751 - D755.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. L. Whetzel, H. Parkinson, H. C. Causton, L. Fan, J. Fostel, G. Fragoso, L. Game, M. Heiskanen, N. Morrison, P. Rocca-Serra, et al.
The MGED Ontology: a resource for semantics-based description of microarray experiments
Bioinformatics, April 1, 2006; 22(7): 866 - 873.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
U. Sarkans, H. Parkinson, G. G. Lara, A. Oezcimen, A. Sharma, N. Abeygunawardena, S. Contrino, E. Holloway, P. Rocca-Serra, G. Mukherjee, et al.
The ArrayExpress gene expression database: a software engineering and implementation perspective
Bioinformatics, April 15, 2005; 21(8): 1495 - 1501.
[Abstract] [Full Text] [PDF]

Home page
 Circ. Res.Home page
C. A. Simmons, G. R. Grant, E. Manduchi, and P. F. Davies
Spatial Heterogeneity of Endothelial Phenotypes Correlates With Side-Specific Vulnerability to Calcification in Normal Porcine Aortic Valves
Circ. Res., April 15, 2005; 96(7): 792 - 799.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
P. White, J. E. Brestelli, K. H. Kaestner, and L. E. Greenbaum
Identification of Transcriptional Networks during Liver Regeneration
J. Biol. Chem., February 4, 2005; 280(5): 3715 - 3722.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.