Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters
Figure 5
CMMR linked Gaggled tools I: Gene Network, Data Matrix Viewer, Bicluster Network.
Expanding the Gaggle tools tab on the BiclusterCard for multi-species bicluster E. coli – S. Typhimurium bicluster 57, reveals a list of links (buttons) to the various Gaggle tools. (A) The Gene Associations button opens a Cytoscape goose that displays the core genes subnetwork for eco57 (top) and stm57 (bottom). The nodes represent genes and edges represent associations based on data from the compendium, indicated in yellow is gene yjjI. Edges are shared annotations: COG code (pink), Prolinks phylogenetic profile (purple), metabolic pathway (blue), operon (light cyan), and Predictome phylogenetic pattern (dark cyan). (B) The expression profiles for the genes and conditions from eco57 (top) and stm57 (bottom) can be explored by opening the Data Matrix Viewer. Using the FireGoose, the bicluster's genes and conditions can be broadcast from the BiclusterCard. We can see how the expression profile of gene yjjI (indicated by the colored line) matches other profiles in the bicluster. (C) The Bicluster Network button opens a Cytoscape goose to display the complete bicluster network where each node is a bicluster (width and height proportional to number of genes and conditions, respectively) and edges represent any shared properties and annotations. We can explore the related bicluster subnetwork for bicluster 57 (yellow), eco57 (left) and stm57 (right), by broadcasting the list of related biclusters (using the FireGoose) from the BiclusterCard to select those biclusters and display them in a new window. There are 10 additional biclusters in the eco57 subnetwork. Node fill color represents significant COG annotation, border color represents significant GO annotation, node border thickness represents residual, and edge color represents shared COG (green) KEGG (red), or GO (blue) annotations.