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Tutorial

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• Install Cytoscape and MiMI Plugin
• Loading a network
• Getting literature information for selected edge and sort the result
• Finding pathway matches for chosen network
• Adding your own node/edge annotation
• Expanding a network
• Finding paths among given genes

Install Cytoscape and MiMI Plugin

Click here to get instructions.

Loading a Network

1. Assuming that you already installed Cytoscape and MiMI Plugin. If you need to install Cytoscape, click here.
   
2. Prepare a list of genes, see, for example mygene.txt .
3. Load mygene.txt file.
   a) Starting up Cytoscape->plugins->MiMI->MiMI Plugin->From File tab-> Drop down box ->specify species, molecule type etc
   b) Load Gene File->your gene file name
   
   
4. Browse node/edge attributes with Cytoscape Node Attribute Browser and Edge Attribute Browser.
   a) Click Node Attribute Browser on Cytoscape panel (bottom right)->click icon ->check attributes name->choose nodes to see attributes.
   b) Click Edge Attribute Browser to get edge information
   
   
5. Double clicking node/edge will direct you to MiMI webpage for that node/edge.

 

Getting literature information for selected edge (interaction) and sort the result

1. Assuming that you already loaded a network. If you need to load a network, click here.
2. Right click an edge->get literature info from BioNLP
   
   
3. Sort the result. Click “sort” to sort the result with MEAD

Finding pathway matches for chosen network

1. Assuming that you already loaded a network. If you need to load a network, click here.
2. Select nodes and edges->right click node->SAGA->apply SAGA to chosen network->specify database and matching percentage->query
   
   
   Adding your own node/edge annotation

1. Assuming that you already loaded a network. If you need to load a network, click here.
2. Right click a node/edge->annotation->log in->change annotation set name->edit attributes from MiMI, add comments and URLs->save->log out
   
   

Expanding a network

1. There is interaction level drop-down list on the dialog box. It has three levels from 1 to 3 that mean users can choose different number of steps of expansion to find neighbors. Choose higher level to expand network.
   
   

Finding paths among given genes

1. If you only interested in interactions among given genes, you can do this by following “Loading a network” and you need to check the box of “Search Paths Between Genes”.