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GeneCodis (RRID:SCR_006943)

Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology.


functional analysis, gene, annotation, statistical analysis, functional genomics

Resource ID


Alternate IDs

nlx_149254, OMICS_02221

Website Status

Last checked up




drosophila melanogaster, caenorhabditis elegans, saccharomyces cerevisiae, arabidopsis thaliana, escherichia coli, bos taurus, candida albicans, zebrafish, chicken, human, leishmania major, mouse, rat, schizosaccharomyces pombe, trypanosoma brucei, vibrio cholerae

Resource Type

Resource, data analysis service, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

Funding Information

Juan de la Cierva research program, Spanish Minister of Science and Innovation | BIO2010-17527, Government of Madrid | P2010/BMD-2305


Free for academic use, Acknowledgement requested


GeneCodis - Gene annotations co-ocurrence discovery, Gene annotations co-ocurrence discovery

Proper citation

(GeneCodis, RRID:SCR_006943)

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GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information.

  • Nogales-Cadenas R
  • Nucleic Acids Res.
  • 2009 Jul 30

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

GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists.

  • Carmona-Saez P
  • Genome Biol.
  • 2007 Mar 29

We present GENECODIS, a web-based tool that integrates different sources of information to search for annotations that frequently co-occur in a set of genes and rank them by statistical significance. The analysis of concurrent annotations provides significant information for the biologic interpretation of high-throughput experiments and may outperform the results of standard methods for the functional analysis of gene lists. GENECODIS is publicly available at

GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics.

  • Tabas-Madrid D
  • Nucleic Acids Res.
  • 2012 Jul 28

Since its first release in 2007, GeneCodis has become a valuable tool to functionally interpret results from experimental techniques in genomics. This web-based application integrates different sources of information to finding groups of genes with similar biological meaning. This process, known as enrichment analysis, is essential in the interpretation of high-throughput experiments. The frequent feedbacks and the natural evolution of genomics and bioinformatics have allowed the growth of the tool and the development of this third release. In this version, a special effort has been made to remove noisy and redundant output from the enrichment results with the inclusion of a recently reported algorithm that summarizes significantly enriched terms and generates functionally coherent modules of genes and terms. A new comparative analysis has been added to allow the differential analysis of gene sets. To expand the scope of the application, new sources of biological information have been included, such as genetic diseases, drugs-genes interactions and Pubmed information among others. Finally, the graphic section has been renewed with the inclusion of new interactive graphics and filtering options. The application is freely available at

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