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ModuleGraph - Documentation

Contents

• Network
• Visual Style


• Module Data
• Defining new Modules and Importing Module Data
• Save and Load Module Data
• Display Module Data


• Module Scores
• Module Representation Score
• Module Connectivity Score

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Network

Creating a ModuleGraph Network

After the module data are loaded (see 'Module Data' section), there are two possibilities to create a ModuleGraph network:

• To create a completely new network, choose ModuleGraph -> Network -> Create Network From File. This option lets you choose a .sif file that defines the network. ModuleGraph will automatically incorporate all modules from the currently loaded data it can find in that network.
• To show the modules in an already existing network, choose ModuleGraph -> Network -> Find Modules In Current Network.

Both options will apply the default ModuleGraph visual style to the network, described in the Visual Style section below.

Visual Style

For a newly created network ModuleGraph will automatically use a force-directed layout. The parameters of that layout are chosen to arrange the network such that modules are close to their constituents. By default, ModuleGraph will show the different entities and relationships in a network as follows:

Entity / Relationship	Explanation	Representation
Modules	A module is an aggregation of multiple elements. For instance a protein complex in a protein network.	Quadratic green nodes
Elements	An element can (but does not have to) be part of a module. For instance a protein in a protein network.	Round blue nodes
Inter element	There exists some relationship between two elements. For instance a regulatory relationship between two genes in a gene regulatory network.	Thin blue edges
Overlap	Two modules have some elements in common. For instance, two protein complexes (can) have the same attachment.	Thick green edges
Belongs to	An element can belong to a module.	Thin black edges

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