M-Finder is an interactive web application to visualize the functional association pattern (i.e., the functional module) of a gene entered by a user.
M-Finder has two major technical components: weighting genome-wide protein-protein interaction data by measuring semantic similarity and simulating information propagation on the weighted protein-protein interaction network by the flow-based graph clustering algorithm.
P-Finder provides detailed information about each gene and each edge in the visualized network.
Follow the instruction below.
Select a species.
Type a gene name or symbol into the Seed Gene box.
Select a weighting method to measure the sematic similarity of interacting gene pairs.
Type a minimum association threshold into the Parameter box. The range of the threshold is between 0 and infinity. The larger the threshold, the smaller the visualized network. (The default threshold is 20.)
Click "RUN" to visualize the functional module. (It takes 20 ~ 40 seconds.)
Increase the minimum association threshold to visualize a smaller network (or if having a message "Too many nodes. Please try again." or "Timeout."), or decrease the threshold to visualize a larger network (or if having a message "Empty network. Please try again.").
Click any gene or interaction on the visualized network to obtain its detailed information.
Drag any node or edge to re-structure the visualized network.
Click "DOWNLOAD" to save the visualized network to an image file.