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.
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.
Authors: Chia-Lin Wei; Patrick Ng; Kuo Ping Chiu; Chee Hong Wong; Chin Chin Ang; Leonard Lipovich; Edison T Liu; Yijun Ruan Journal: Proc Natl Acad Sci U S A Date: 2004-07-22 Impact factor: 11.205
Authors: Israel T Silva; Ricardo Z N Vêncio; Thiago Y K Oliveira; Greice A Molfetta; Wilson A Silva Journal: BMC Bioinformatics Date: 2010-03-30 Impact factor: 3.169
Authors: Marion Cornelissen; Antoinette C van der Kuyl; Remco van den Burg; Fokla Zorgdrager; Carel J M van Noesel; Jaap Goudsmit Journal: BMC Cancer Date: 2003-03-18 Impact factor: 4.430
Authors: Antoinette C van der Kuyl; Remco van den Burg; Fokla Zorgdrager; John T Dekker; Jolanda Maas; Carel J M van Noesel; Jaap Goudsmit; Marion Cornelissen Journal: BMC Cancer Date: 2002-09-02 Impact factor: 4.430