Figure 2

Schematic overview of the additional information provided by Prosecutor. Various layers of information are supplied for the iGBA results (2A) from Prosecutor. Predicted functional assignments for genes whose operon members are already linked to the predicted function are indicated in the results (2B). In addition, this protocol is also followed for divergent genes that share the same upstream region (in this example pps and ydiA). The operon information that is used for the genomic context analysis is also used to detect known regulatory sequences for transcriptional modules (2C). Lastly, graph visualization is used to visualize the gene redundancy of the different functional assignments of Prosecutor (2D). Nodes in the graph represent functional categories and genes. Arrows represent membership of gene nodes to a functional category node as well as the putative functional prediction of the studied gene. The members of individual categories are placed in colored aggregates. In addition to the aggregates, a colored square is placed in each gene member of a category. The squares are colored using the colors of their matching aggregates. Members of different categories can easily be distinguished using the colored squares. An example of a functional prediction found by Prosecutor for ydiE from E. coli is shown. The expression of this gene was correlated with members of various functional categories involved in the uptake of iron. In addition to the functional association with the transcriptional module Fur, the upstream region of ydiE also contains a putative Fur DNA binding site.