1- General info
GeneCodis is a web-based tool for the functional analysis of lists of genes, proteins, and regulatory elements miRNAs, transcription factors (TFs), and CpGs. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes o miRNAs under study with respect to a reference list. As well as single collections, this tool allows users to simultaneously evaluate annotations from different sources, for example GO Biological Process and KEGG. To this end, and before computing p-values, it uses the associantion rules algorithms to extract sets of annotations that frequently co-occur in the analyzed list of genes. More information can be found in Carmona-Saez et al. (BMC Bioinformatics, 2006).
You are visiting a whole new website of GeneCodis. This new version, the fourth, allows users to input genes, proteins, TFs, CpG sites and miRNAs. This has suppoused a complete update in the statistical methods to overcome a known gene selection bias with the Wallenius approach. It is present in the set enrichment analysis of regulatory elements that need to be transformed to their associated genes to test the annotations and exceptionally with genes selected from expression data obtained with aggregated tag counts. The new methods are based on GOseq.
We have updated the annotations and organisms. Annotations are now divided in four general collections, Functional, Regulatory with miRNAs-based annotations, Drugs and Phenotypes. The results are also displayed differently, we are now using D3.js to create two interactive visualizations, a gene-, mirna-annotation network and a bars chart.
In case that you are missing any functionality, organisms, annotation or even if you want some kind of new feature please do not hesitate in contact us at firstname.lastname@example.org since we are continually working on creating a complete updated GeneCodis, feedback is always appreciated.