g<Emphasis FontCategory="NonProportional">raphite</Emphasis> - a Bioconductor package to convert pathway topology to gene network |
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| Authors: | Gabriele Sales Enrica Calura Duccio Cavalieri Chiara Romualdi |
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| Institution: | (1) Department of Biology, University of Padova, via U. Bassi 58/B, Padova, Italy;(2) Department of Computational Biology, Istituto Agrario di San Michele all’Adige, Trento, Italy |
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| Abstract: | Background Gene set analysis is moving towards considering pathway topology as a crucial feature. Pathway elements are complex entities
such as protein complexes, gene family members and chemical compounds. The conversion of pathway topology to a gene/protein
networks (where nodes are a simple element like a gene/protein) is a critical and challenging task that enables topology-based
gene set analyses. |
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