The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. - Inserm - Institut national de la santé et de la recherche médicale Accéder directement au contenu
Article Dans Une Revue BMC Bioinformatics Année : 2008

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology.

Résumé

BACKGROUND: High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. RESULTS: We developed the Annotation, Mapping, Expression and Network (AMEN) software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i) uploading and pre-processing data from microarray expression profiling experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. CONCLUSION: AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.
Fichier principal
Vignette du fichier
1471-2105-9-86.pdf (1.07 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Loading...

Dates et versions

inserm-00521445 , version 1 (29-09-2010)

Identifiants

Citer

Frédéric Chalmel, Michael Primig. The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology.. BMC Bioinformatics, 2008, 9, pp.86. ⟨10.1186/1471-2105-9-86⟩. ⟨inserm-00521445⟩
119 Consultations
318 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More