title: GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information.
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.es.
authors.affiliation: Computer Architecture Department, Complutense University of Madrid, Madrid, Spain.
authors.forename: Ruben
authors.initials: R
authors.lastname: Nogales-Cadenas
authors.forename: Pedro
authors.initials: P
authors.lastname: Carmona-Saez
authors.forename: Miguel
authors.initials: M
authors.lastname: Vazquez
authors.forename: Cesar
authors.initials: C
authors.lastname: Vicente
authors.forename: Xiaoyuan
authors.initials: X
authors.lastname: Yang
authors.forename: Francisco
authors.initials: F
authors.lastname: Tirado
authors.forename: Jose María
authors.initials: JM
authors.lastname: Carazo
authors.forename: Alberto
authors.initials: A
authors.lastname: Pascual-Montano
mesh_terms: D000818:Animals; D002417:Cattle; D005786:Gene Expression Regulation; D005796:Genes; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism; D051381:Rats; D012984:Software; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors