Tutorial


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
    Tutorial image 0
  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
    Tutorial image 1
  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
    Tutorial image 3
  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
    Tutorial image 4
    Tutorial SAGA results image
    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
    Tutorial image 4
    Tutorial image 10

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.
    Tutorial image 7


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”.
    Tutorial image 8



Top of Page