Interactome for a single protein

This panel shows the top interactions for a selected protein in the selected species. The width of the edges is proportional to the selected score. The node and interaction controls on the left allow you to get information about the selected node/interaction and to add them to a list of selected nodes/interactions. This list of interactions can be downloaded as a text file.

Top interactome per predictor

This panel shows the top interactions for the selected species based on the chosen predictor in the "Prioritize using" input. Filters are available to remove interactions with ribosomal proteins and to only include interactions with proteomic support (within top 5% of at least one proteomic predictor). The width of the edges is proportional to the selected score. The node and interaction controls on the left allow you to get information about the selected node/interaction and to add them to a list of selected nodes/interactions. This list of interactions can be downloaded as a text file.

This panel shows the orthologs of a selected complex in the selected species. Orthologs are obtained from BioCyc. Additional proteins can be incorporated using the slider. If the average interactions checkbox is selected, the additional proteins are selected based on the average score of the selected predictor for all orthologs. Otherwise the stronger interaction to any ortholog is selected. Nodes and interactions in the bacteroides network can be explored and added to a list of selected nodes/interactions as in the interactome panel.

E. coli complex
Bacteroides complex
XL-MS data

This panel shows the crosslinking data for the selected species. The edge width is proportional to the number of crosslinked peptides between two proteins. As many experiments were performed, interactions from specific experiments can be selected using the dropdown menu. Please be sure to match experiment to the species in the left menu, Otherwise interaction reports will not work.

Candidates for AP-MS

This panel shows the top candidates for AP-MS validation. The rank can be selected using the dropdown menu for a given species. To select these candidates, we first select the top 12k interactions as per the ensemble score. Next, ribosomal interactions and essential proteins are removed from the network and all the nodes are ranked by clustering coefficient, which measures how connected the first order neighbor of a node are. For every rank, the candidate protien is highlighted in yellow.