GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information
Open Access
- 22 May 2009
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 37 (Web Server), W317-W322
- https://doi.org/10.1093/nar/gkp416
Abstract
GeneCodis is a web server application for functional analysis of gene lists that integrates different sources of information and finds modular patterns of interrelated annotations. This integrative approach has proved to be useful for the interpretation of high-throughput experiments and therefore a new version of the system has been developed to expand its functionality and scope. GeneCodis now expands the functional information with regulatory patterns and user-defined annotations, offering the possibility of integrating all sources of information in the same analysis. Traditional singular enrichment is now permitted and more organisms and gene identifiers have been added to the database. The application has been re-engineered to improve performance, accessibility and scalability. In addition, GeneCodis can now be accessed through a public SOAP web services interface, enabling users to perform analysis from their own scripts and workflows. The application is freely available at http://genecodis.dacya.ucm.esThis publication has 15 references indexed in Scilit:
- FactorY, a bioinformatic resource for genome-wide promoter analysisComputers in Biology and Medicine, 2009
- GENECODIS: a web-based tool for finding significant concurrent annotations in gene listsGenome Biology, 2007
- Functional Interpretation of Microarray ExperimentsOMICS: A Journal of Integrative Biology, 2006
- BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experimentsNucleic Acids Research, 2006
- Integrated analysis of gene expression by association rules discoveryBMC Bioinformatics, 2006
- Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profilesProceedings of the National Academy of Sciences of the United States of America, 2005
- Ontological analysis of gene expression data: current tools, limitations, and open problemsBioinformatics, 2005
- Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammalsNature, 2005
- DAVID: Database for Annotation, Visualization, and Integrated DiscoveryGenome Biology, 2003
- Gene Ontology: tool for the unification of biologyNature Genetics, 2000