Bioinformatics Vol. 16 no. 10 2000
Pages 899-905
© 2000 Oxford University Press
Original Paper |
USAGE: a web-based approach towards the analysis of SAGE data
1 Bioinformatics Laboratory
2 Laboratory of Pediatric Endocrinology
3 Department of Pediatric Oncology
4 Department of Anatomy and Embryology
5 Department of Human Genetics
6 Department of Clinical Epidemiology and
Biostatistics
7 Neurozintuigen Laboratory, Academic
Medical Center, Meibergdreef 9, 1100 AZ Amsterdam, The Netherlands
8 Centre for Molecular and Biomolecular
Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED
Nijmegen, The Netherlands
Received on April 11, 2000
; accepted on May 22, 2000
Motivation: SAGE enables the determination of genome-wide mRNA expression profiles. A comprehensive analysis of SAGE data requires software, which integrates (statistical) data analysis methods with a database system. Furthermore, to facilitate data sharing between users, the application should reside on a central server and be accessed via the internet. Since such an application was not available we developed the USAGE package.
Results: USAGE is a web-based application that comprises an integrated set of tools, which offers many functions for analysing and comparing SAGE data. Additionally, USAGE includes a statistical method for the planning of new SAGE experiments. USAGE is available in a multi-user environment giving users the option of sharing data. USAGE is interfaced to a relational database to store data and analysis results. The USAGE query editor allows the composition of queries for searching this database. Several database functions have been included which enable the selection and combination of data. USAGE provides the biologist increased functionality and flexibility for analysing SAGE data.
Availability: USAGE is freely accessible for academic institutions at http://www.cmbi.kun.nl/usage/. The source code of USAGE is freely available for academic institutions on request from the first author.
Contact: a.h.vankampen{at}amc.uva.nl
To whom correspondence should be addressed.
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