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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.<\/jats:p>\n            <jats:p>Unfortunately, currently available R\/Bioconductor packages provide pathway networks only from single databases. They do not propagate signals through chemical compounds and do not differentiate between complexes and gene families.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here we present , a Bioconductor package addressing these issues. Pathway information from four different databases is interpreted following specific biologically-driven rules that allow the reconstruction of gene-gene networks taking into account protein complexes, gene families and sensibly removing chemical compounds from the final graphs. The resulting networks represent a uniform resource for pathway analyses. Indeed, graphite provides easy access to three recently proposed topological methods. The  package is available as part of the Bioconductor software suite.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p> is an innovative package able to gather and make easily available the contents of the four major pathway databases. In the field of topological analysis  acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-20","type":"journal-article","created":{"date-parts":[[2012,1,31]],"date-time":"2012-01-31T14:57:34Z","timestamp":1328021854000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":183,"title":["graphite - a Bioconductor package to convert pathway topology to gene network"],"prefix":"10.1186","volume":"13","author":[{"given":"Gabriele","family":"Sales","sequence":"first","affiliation":[]},{"given":"Enrica","family":"Calura","sequence":"additional","affiliation":[]},{"given":"Duccio","family":"Cavalieri","sequence":"additional","affiliation":[]},{"given":"Chiara","family":"Romualdi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,1,31]]},"reference":[{"key":"5051_CR1","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1186\/1471-2105-10-47","volume":"10","author":"M Ackermann","year":"2009","unstructured":"Ackermann M, Strimmer K: A general modular framework for gene set enrichment analysis. 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