Interpreting the gene expression microarray results: a user-based evaluation of 10 bioinformatics tools

Oligonucleotide and cDNA microarrays are highthroughput techniques that compare the mRNA expression of a large group of genes in different cells or experimental conditions. The final output of a microarray data analysis is a list of codes identifying differentially expressed transcripts. Interactions among genes, however, are not adequately represented by a list of codes. Therefore, the following step of a microarray experiment is the biological interpretation of results to formulate hypotheses on the molecular mechanisms underlying the investigated biological phenomenon. To deal with this challenging task, users submit the complete list of differentially expressed genes (DEGs) to several bioinformatics tools that query specific databases of biological information. by these tools, the investigators usually expect to obtain: a) an exhaustive annotation of as many as possible DEGs, b) an effective visualization of the biological interactions among DEGs, c) some suggestions on what are the most important groups of interacting DEGs and the biological processes in which they are involved. To date, a tool that meets all these requirements does not exist and users have to cope with many different tools in order to obtain all the needed information. Interpreting the gene expression microarray results: a user-based evaluation of 10 bioinformatics tools