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

Abstract

In recent years many tools have been developed to cope with the interpretation of gene expression results from microarray experiments. The effectiveness of these tools largely depends on their ease of use by biomedical researchers. Tools based on effective computational methods, indeed, cannot be fully exploited by users if they are not supported by an intuitive interface, a large set of utilities and effective outputs. In this paper, ten tools for the interpretation of gene expression microarray results have been tested on eleven microarray datasets and evaluated according to eight assessment criteria: 1. interface design and usability, 2. easiness of input submission, 3. effectiveness of output representation, 4. efficacy of the downloaded outputs, 5. possibility to submit multiple gene IDs, 6. sources of information, 7. provision of different statistical tests and 8. supply of multiple test correction methods. Strengths and weaknesses of each tool are highlighted: a. to provide useful tips to users dealing with the biological interpretation of microarray results; b. to draw the attention of software developers on the usability of their tools.