Journal of Proteomics & Bioinformatics
Open Access

Abstract

GExMap: An Intuitive Visual Tool to Detect and Analyze Genomic Distribution in Microarray-generated Lists of Differentially Expressed Genes

Nicolas Cagnard, Carlo Lucchesi and Gilles Chiocchia

High- throughput technologies, as DNA microarrays, generate a huge amount of data, which are difficult to interpret. Biologists require easy-to-use tools to analyze them and explore new scientific hypotheses. We propose a visual data mining tool to extract a new type of useful genomic information buried in gene lists generated by differential expression studies. We compare the genomic distribution that is observed within the gene list with the expected distribution, which is estimated from public genomic databases. An algorithm of research and a statistical test give reliable and optimal results. GExMap helps identify genomic regions that are enriched in genes whose differential expression is of potential interest for target diseases. This software is freely available20 and easily customized. Since sources are frequently updated, it offers tools for updates at any moment. GExMap is usable by any commercially and publicly available microarray platform. Furthermore, GExMap helps in interpretation by showing an ordered list for each gene ontology. Presently, GExMap can also be used to analyse gene lists not only from the Homo sapiens genome but also the Mus musculus and the Rattus norvegicus genomes.