Interpreting the gene expression microarray results: a user-based experience.
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, 10 tools for the interpretation of gene expression microarray results have been tested on 11 microarray datasets and evaluated according to eight assessment criteria: 1. interface design and usability, 2. easiness of input submission, 3. effectiveness of output representation and 4. of the downloaded outputs, 5. possibility to submit multiple gene IDs, 6. sources of information, 7. provision of different statistical tests and 8. of multiple test correction methods. Strengths and weaknesses of each tool are highlighted to: a. provide useful tips to users dealing with the biological interpretation of microarray results; b. draw the attention of software developers on the usability of their tools.
Microarray Lab, Department of Surgical, Medical and Molecular Pathology and of Critical Area, University of Pisa, Pisa, Italy Email: erika.melissari@for.unipi.it, silvia.pellegrini@med.unipi.it.
Erika
E
Melissari
Manuela
M
Di Russo
Veronica
V
Mariotti
Marco
M
Righi
Caterina
C
Iofrida
Silvia
S
Pellegrini
D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D015870:Gene Expression; D006801:Humans; D046228:Microarray Analysis; D012984:Software; D014584:User-Computer Interface