mDAG: a web-based tool for analyzing microarray data with multiple treatments
TL;DR: This work employs directed graphs to represent gene response to pairs of treatments in microarray experiments involving multiple treatments and has been applied and found useful in identifying and differentiating genes sharing similar functional pathways.
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Abstract: 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 [1,2].
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References
Chemical genomics of cancer chemopreventive dithiolethiones.
Quynh T. Tran,Lijing Xu,Vinhthuy Phan,Shirlean Goodwin,Mohammed Mostafizur Rahman,Victor X. Jin,Carrie Hayes Sutter,Bill D. Roebuck,Thomas W. Kensler,E. Olusegun George,Thomas R. Sutter +10 more
TL;DR: Functional analysis revealed that OLT and TBD, in addition to their effects on CYP, modulate liver lipid metabolism, especially fatty acids, and provide new insight into the actions of clinically relevant and lead dithiolethione analogues.
Analyzing microarray data with transitive directed acyclic graphs.
Vinhthuy Phan,E. Olusegun George,Quynh T. Tran,Shirlean Goodwin,Sridevi Bodreddigari,Thomas R. Sutter +5 more
TL;DR: The usage of transitive directed acyclic graphs (tDAG) is proposed as the representation of these patterns and it is shown that such representation can be useful in clustering treatment effects, annotating existing clustering methods, and analyzing sample sizes.
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