Our multi-level integration approach first links all intermediate information to either the central functional wrapper (as defined by the eggNOG database) or to the central structural wrapper (as defined by the PDB database).
Using a compendium of microarray gene expression data from the M3D database [30], networks were constructed for the 27 genes contained in the ROS pathway as defined by the EcoCyc database [1] (Figure 2).
Moreover, the triples only attach this drug role to approved drugs, as defined by the ChEMBL database.
The output map was masked based on the actual forest distribution as defined by the CORINE Land Cover database.
Areas shown as loss (between 2005 and 2010) were considered to be deforested, and were summed across level-one subnational administrative units as defined by the GADM (Database of Global Administrative Areas; political boundaries reflecting states or districts).
EMBL-Bank format uses a different syntax to the records in DDBJ and GenBank, though each format uses certain standardised nomenclature, such as taxonomies as defined by the NCBI Taxon database.
Here, we focus on cysteine proteases of the CE clan [11], as defined by the MEROPS database [12].
To investigate this, we grouped all proteins belonging to the same functional category (as defined by the STRING database [18]) and counted the links within these groups and between groups.
The ORFs of R. conorii whose expression was significantly altered were classified into functional categories according to the Cluster of Orthologous Gene (COG) classification, as defined by the COGs database [15].
When comparing a manually curated set of dosage sensitive genes derived from the scientific literature, we found that a significantly larger than expected proportion of these genes were members of a protein complex as defined by the CORUM database.
It contains the two N- and C-domains of arrestins as defined by the PFAM database and modeling of its arrestin core onto the structure of mammalian β-arrestin 1 indicates that despite poor sequence conservation with canonical arrestins, AdcA adopts a similar fold.
