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

By Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, J. M. Carazo, Alberto Domingo Pascual-Montano. Genome Biology, 2007

626 citations recorded by the source corpus.

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 http://genecodis.dacya.ucm.es/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c5926f44b41bb98b8aee35b95c3531ce8be0febf

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists (2008, positive): “Recent tools, such as Ontologizer (69), topGO (41), GENECODIS (59), ADGO (45) and ProfCom (68), claimed to improve discovery sensitivity and speciﬁcity by considering inter-relationships of GO terms in the enrichment calculations, i.e. using genes of composite (joint) annotation terms as a…”
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases (2011, background): “A growing number of tools have been developed for pathway and disease identiﬁcation, including, but not limited to, MAPPFinder (13), EASE (14), DAVID (15,16), ArrayXPath (17), WebGestalt (18), FuncCluster (19), PageMan (20), GENECODIS (21,22), GeneTrail (23), g:Proﬁler (24), FunNet (25) and PaLS (26”
The mathematics of tanning (2009, positive): “Gene Ontology based associations were computed with Genecodis [65].”
GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information (2009, methodology): “In 2007, we introduced GeneCodis (7), a tool for modular enrichment analysis oriented to integrate information from different sources and find enriched combinations of annotations in large lists of genes or proteins.”
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics (2012, methodology): “As shown in (12), there are biological terms not detected as statistically relevant when tested individually, which turn out to be significant when appearing together with others.”
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling (2010, methodology): “Thus, the Genecodis method (33) that finds concurrent annotations in ranked lists of genes is one of the new methods included.”
Reprogramming of the Circadian Clock by Nutritional Challenge (2013, neutral): “Gene annotation was performed using Genecodis (Carmona-Saez et al., 2007; Nogales- Cadenas et al., 2009).”