Using Firegoose to investigate transcription response of H. salinarum to anoxic conditions. A list of genes with similar expression profiles is found by microarray analysis. (1) We broadcast these genes to KEGG to query for known biochemical pathways, for example, viewing the Arginine and proline metabolism pathway. (2) We broadcast the genes to EMBL STRING, a protein interaction database, where we can (3) navigate to functionally related genes. (4) In order to manipulate the network, we broadcast it to Cytoscape. (5) A local database provides additional information. (6) DAVID performs functional clustering. (7) For one cluster containing signal transduction genes, we use String's links to protein domains.
Bare et al. BMC Bioinformatics 2007 8:456 doi:10.1186/1471-2105-8-456