Pomelo II: Finding differentially expressed genes
Entity
UAM. Departamento de BioquímicaPublisher
Oxford University PressDate
2009-08-04Citation
10.1093/nar/gkp366
Nucleic Acids Research 37.SUPPL. 2 (2009): W581–W586
ISSN
0305-1048 (print); 1362-4962 (online)DOI
10.1093/nar/gkp366Funded by
Fundación de Investigación Médica Mutua Madrileña and Project [TIC2003-09331-C02-02 of the Spanish Ministry of Education and Science (MEC); Red Temática de Investigación Cooperativa COMBIOMED.Project
Gobierno de España. TIC2003-09331-C02-02Editor's Version
http://dx.doi.org/10.1093/nar/gkp366Subjects
Pomelo II; Gene; Gene Ontology; KEGG and Reactome pathways; MedicinaRights
© 2009 The Author(s)Abstract
Pomelo II (http://pomelo2.bioinfo.cnio.es) is an open-source, web-based, freely available tool for the analysis of gene (and protein) expression and tissue array data. Pomelo II implements: permutation-based tests for class comparisons (t-test, ANOVA) and regression; survival analysis using Cox model; contingency table analysis with Fisher's exact test; linear models (of which t-test and ANOVA are especial cases) that allow additional covariates for complex experimental designs and use empirical Bayes moderated statistics. Permutation-based and Cox model analysis use parallel computing, which permits taking advantage of multicore CPUs and computing clusters. Access to, and further analysis of, additional biological information and annotations (PubMed references, Gene Ontology terms, KEGG and Reactome pathways) are available either for individual genes (from clickable links in tables and figures) or sets of genes. The source code is available, allowing for extending and reusing the software. A comprehensive test suite is also available, and covers both the user interface and the numerical results. The possibility of including additional covariates, parallelization of computation, open-source availability of the code and comprehensive testing suite make Pomelo II a unique tool.
Files in this item
Google Scholar:Morrissey, Edward R.
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Díaz Uriarte, Ramón
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