Browsing by Author "Shasha, Dennis E."

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    Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
    (2007) Gutierrez, Rodrigo A.; Lejay, Laurence V.; Dean, Alexis; Chiaromonte, Francesca; Shasha, Dennis E.; Coruzzi, Gloria M.
    Background: Carbon (C) and nitrogen (N) metabolites can regulate gene expression in Arabidopsis thaliana. Here, we use multinetwork analysis of microarray data to identify molecular networks regulated by C and N in the Arabidopsis root system.
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    Sungear
    (2007) Poultney, Christopher S.; Gutierrez, Rodrigo A.; Katari, Manpreet S.; Gifford, Miriam L.; Paley, W. Bradford; Coruzzi, Gloria M.; Shasha, Dennis E.
    Sungear is a software system that supports a rapid, visually interactive and biologist-driven comparison of large datasets. The datasets can come from microarray experiments (e.g. genes induced in each experiment), from comparative genomics (e.g. genes present in each genome) or even from non-biological applications (e.g. demographics or baseball statistics). Sungear represents multiple datasets as vertices in a polygon. Each possible intersection among the sets is represented as a circle inside the polygon. The position of the circle is determined by the position of the vertices represented in the intersection and the area of the circle is determined by the number of elements in the intersection. Sungear shows which Gene Ontology terms are over-represented in a subset of circles or anchors. The intuitive Sungear interface has enabled biologists to determine quickly which dataset or groups of datasets play a role in a biological function of interest.