g<monospace>raphite</monospace> - a Bioconductor package to convert pathway topology to gene network
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-01-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/13/20 |
| _version_ | 1811314563817144320 |
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| author | Sales Gabriele Calura Enrica Cavalieri Duccio Romualdi Chiara |
| author_facet | Sales Gabriele Calura Enrica Cavalieri Duccio Romualdi Chiara |
| author_sort | Sales Gabriele |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <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.</p> <p>Results</p> <p>Here we present <monospace>graphite</monospace>, 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 <monospace>graphite</monospace> package is available as part of the Bioconductor software suite.</p> <p>Conclusions</p> <p><monospace>graphite</monospace> 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 <monospace>graphite</monospace> acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements.</p> |
| first_indexed | 2024-04-13T11:13:48Z |
| format | Article |
| id | doaj.art-e5d0be6ea7494451a03206d197ca192f |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T11:13:48Z |
| publishDate | 2012-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-e5d0be6ea7494451a03206d197ca192f2022-12-22T02:49:02ZengBMCBMC Bioinformatics1471-21052012-01-011312010.1186/1471-2105-13-20g<monospace>raphite</monospace> - a Bioconductor package to convert pathway topology to gene networkSales GabrieleCalura EnricaCavalieri DuccioRomualdi Chiara<p>Abstract</p> <p>Background</p> <p>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.</p> <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.</p> <p>Results</p> <p>Here we present <monospace>graphite</monospace>, 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 <monospace>graphite</monospace> package is available as part of the Bioconductor software suite.</p> <p>Conclusions</p> <p><monospace>graphite</monospace> 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 <monospace>graphite</monospace> acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements.</p>http://www.biomedcentral.com/1471-2105/13/20 |
| spellingShingle | Sales Gabriele Calura Enrica Cavalieri Duccio Romualdi Chiara g<monospace>raphite</monospace> - a Bioconductor package to convert pathway topology to gene network BMC Bioinformatics |
| title | g<monospace>raphite</monospace> - a Bioconductor package to convert pathway topology to gene network |
| title_full | g<monospace>raphite</monospace> - a Bioconductor package to convert pathway topology to gene network |
| title_fullStr | g<monospace>raphite</monospace> - a Bioconductor package to convert pathway topology to gene network |
| title_full_unstemmed | g<monospace>raphite</monospace> - a Bioconductor package to convert pathway topology to gene network |
| title_short | g<monospace>raphite</monospace> - a Bioconductor package to convert pathway topology to gene network |
| title_sort | g monospace raphite monospace a bioconductor package to convert pathway topology to gene network |
| url | http://www.biomedcentral.com/1471-2105/13/20 |
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