1471-2105-12-S7-A7 1471-2105 Meeting abstract <p>mDAG: a web-based tool for analyzing microarray data with multiple treatments</p> Phan T Vinhthuy vphan@memphis.edu Vo S Nam Sutter R Thomas

Department of Computer Science, University of Memphis, Memphis, TN, 38152, USA

Bioinformatics Program, University of Memphis, Memphis, TN, 38152, USA

Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA

 BMC Bioinformatics <p>UT-ORNL-KBRIN Bioinformatics Summit 2011</p> Eric C Rouchka, Robert M Flight and Ramin Homayouni Meeting abstracts - A single PDF containing all abstracts in this Supplement is available here. http://www.biomedcentral.com/content/pdf/1471-2105-12-S7-info.pdf <p>10<sup>th</sup> Annual UT-ORNL-KBRIN Bioinformatics Summit 2011</p> Memphis, TN, USA 1-3 April 2011 http://citg.uthsc.edu/summit_11/program.html 1471-2105 2011 12 Suppl 7 A7 http://www.biomedcentral.com/1471-2105/12/S7/A7 10.1186/1471-2105-12-S7-A7 5 8 2011 2011 Phan et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Background

In microarray experiments involving multiple treatments, pairwise comparisons between all pairs of treatments are desirable but expensive. To cope with this, we previously introduced a method that performed all pairwise comparisons in a post hoc manner. This method employs directed graphs to represent gene response to pairs of treatments. It has been applied and found useful in identifying and differentiating genes sharing similar functional pathways 12.

Results

mDAG is a web-based software based on this method. mDAG allows users to upload microarray data in GCT format through a web interface. From this data, the application performs calculations to assign graphical patterns to genes and outputs images and textual data for further analyses. These graphical patterns carry specific meanings in terms of how genes respond to pairs of treatments. The application is implemented using Python and web2py.

mDAG is available at http://cetus.cs.memphis.edu:8080/mDAG.

Conclusion

For experiments involved multiple treatments and replicates, mDAG allows researchers to analyze and visualize in graphical representations relationships of gene interactions to all pairs of treatments. The software can be used online or off-line.

Acknowledgements

This software is supported by the Center for Alternatives to Animal Testing at the John Hopkins school of Public Heath, Project CAAT-2011-18.

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