USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression

A. H. van Kampen; B. D. van Schaik; E. Pauws; E. M. Michiels; J. M. Ruijter; H. N. Caron; R. Versteeg; S. H. Heisterkamp; J. A. Leunissen; F. Baas; M. van der Mee

doi:https://doi.org/10.1093/bioinformatics/16.10.899

USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression

A. H. van Kampen, B. D. van Schaik, E. Pauws, E. M. Michiels, J. M. Ruijter, H. N. Caron, R. Versteeg, S. H. Heisterkamp, J. A. Leunissen, F. Baas, M. van der Mee

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Research output: Contribution to journal › Article › Academic › peer-review

37 Citations (Scopus)

Abstract

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

Original language	English
Pages (from-to)	899-905
Journal	Bioinformatics (Oxford, England)
Volume	16
Issue number	10
DOIs	https://doi.org/10.1093/bioinformatics/16.10.899
Publication status	Published - 2000

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https://doi.org/10.1093/bioinformatics/16.10.899

Cite this

van Kampen, A. H., van Schaik, B. D., Pauws, E., Michiels, E. M., Ruijter, J. M., Caron, H. N., Versteeg, R., Heisterkamp, S. H., Leunissen, J. A., Baas, F., & van der Mee, M. (2000). USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression. Bioinformatics (Oxford, England), 16(10), 899-905. https://doi.org/10.1093/bioinformatics/16.10.899

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abstract = "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",

author = "{van Kampen}, {A. H.} and {van Schaik}, {B. D.} and E. Pauws and Michiels, {E. M.} and Ruijter, {J. M.} and Caron, {H. N.} and R. Versteeg and Heisterkamp, {S. H.} and Leunissen, {J. A.} and F. Baas and {van der Mee}, M.",

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AU - van Kampen, A. H.

AU - van Schaik, B. D.

AU - Pauws, E.

AU - Michiels, E. M.

AU - Ruijter, J. M.

AU - Caron, H. N.

AU - Versteeg, R.

AU - Heisterkamp, S. H.

AU - Leunissen, J. A.

AU - Baas, F.

AU - van der Mee, M.

PY - 2000

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N2 - 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

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