Usage

Overview

Biological processes are often performed by a group of proteins rather than by individual proteins, and proteins in a same biological group form a densely connected subgraph in a protein-protein interaction network. Therefore, finding a densely connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program called ModuleSearch for finding cliques and near-cliques in a protein-protein interaction network.

Download

Software: ModuleSearch
Data: 1. Yeast protein-protein interaction data
2. Yeast protein function data
3. Yeast protein complex data

Usage

ModuleSearch runs on any computer system with a Java Development Kit (JDK), version 1.5 or higher. If such a JDK is not installed, download and install one from either Sun's Java site (http://java.sun.com/javase/downloads/index.jsp) or from the IBM Java site (http://www-106.ibm.com/developerworks/java/) before executing ModuleSearch.
Execute ModuleSearch by double clicking the JAR file (ModuleSearch.jar) or by a command like "java -jar ModuleSearch.jar".
Load both protein-protein interactions file (PPI file) and GO annotations file (GO file), Complex file or FunCat file using the Open menu of File.
Set the similarity of nodes of some subgraphs using the Edit menu.
Find modules using the Analysis menu.
Click a module in the module list to get the information of the module.

Input format

PID file
*.pid: protein-protein interaction file. Each line of the file contains a pair of protein names, separated by a tab.

GO file
*.pid: GO annotations file (GO file). Each line of the file contains a protein name and GO term, separated by a tab.

Interface

(A) Main menu and toolbar.
(B) Modules found by ModuleSearch. If you click a module, it lists the proteins of the module.
(C) Interaction network of the proteins in the module selected by the user in pane (B).
(D) Analysis results of a module. The first part of the analysis results shows the GO terms associated with each protein in the module. The last row of the first part shows how many proteins of the module are associated with each GO term (e.g., functional coherence). The second part shows the p-value of the GO term in the module.

	Open PPI file		Open a file of protein-protein interactions in the pid format (pairing format of interacting proteins).
	Open GO file		Open a file of GO annotations in the format "protein GO_annotation" in each line.
	Open project		Open a project generated by the program.
	Save		Save the project in the current location.
	Save As		Save the project in a new location.
	Exit		Terminate the program.

Set the similarity of nodes in a certain topology.

Save: Save the assigned values.
Cancel: Assign zero to all similarities.
Close: Close the dialog box.

Predict and analyze modules.