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GEDI: a user-friendly toolbox for analysis of large-scale gene expression data.

Fujita A, Sato JR, Ferreira CE, Sogayar MC - BMC Bioinformatics (2007)

Bottom Line: GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us.It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations.Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

View Article: PubMed Central - HTML - PubMed

Affiliation: Chemistry Institute, University of São Paulo, Av, Lineu Prestes, 748 - São Paulo, 05508-900, SP, Brazil. fujita@ime.usp.br

ABSTRACT

Background: Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills.

Results: Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al.

Conclusion: GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

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Snapshot of the GEDI interface. The GEDI interface is very simple and practical. One may select the desired analysis tool and then, an interactive window will open requesting the desired parameters for the selected method.
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Related In: Results  -  Collection

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Figure 1: Snapshot of the GEDI interface. The GEDI interface is very simple and practical. One may select the desired analysis tool and then, an interactive window will open requesting the desired parameters for the selected method.

Mentions: Figure 1 illustrates the GEDI interface. The user-friendly interface allows that, with a few clicks, the user may access any analitical method implemented in GEDI. The graphical user interface (GUI) is displayed using the Tcl/Tk library, opening interactive windows where it is possible to easily input the parameters required for each method.


GEDI: a user-friendly toolbox for analysis of large-scale gene expression data.

Fujita A, Sato JR, Ferreira CE, Sogayar MC - BMC Bioinformatics (2007)

Snapshot of the GEDI interface. The GEDI interface is very simple and practical. One may select the desired analysis tool and then, an interactive window will open requesting the desired parameters for the selected method.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194737&req=5

Figure 1: Snapshot of the GEDI interface. The GEDI interface is very simple and practical. One may select the desired analysis tool and then, an interactive window will open requesting the desired parameters for the selected method.
Mentions: Figure 1 illustrates the GEDI interface. The user-friendly interface allows that, with a few clicks, the user may access any analitical method implemented in GEDI. The graphical user interface (GUI) is displayed using the Tcl/Tk library, opening interactive windows where it is possible to easily input the parameters required for each method.

Bottom Line: GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us.It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations.Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

View Article: PubMed Central - HTML - PubMed

Affiliation: Chemistry Institute, University of São Paulo, Av, Lineu Prestes, 748 - São Paulo, 05508-900, SP, Brazil. fujita@ime.usp.br

ABSTRACT

Background: Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills.

Results: Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al.

Conclusion: GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

Show MeSH