NetMatch by Example
Find all "short" paths from proteins located in the plasma membrane to proteins in the nucleus in galfiltered.xgmml network
1) Load GalFiltered.xgmml file from Cytoscape File menu (it is in sampleData directory). |
2) Run NetMatch. |
3) Select drawing tool. |
4) Select "Add Node" from Palette Panel clicking on it with left mouse button. |
5) Add two nodes on drawing canvas (clicking with the left mouse button). |
6) Change the attribute of the first node clicking on it with the right mouse button. |
7) Set the attribute as "plasma membrane" (notice that the tool is case sensitive). |
8) In the same way, change the attribute of the second node in "nucleus". |
9) Select "Add Path" from Palette Panel clicking on it with left mouse button. |
10) Add the path clicking with the left button, first on "plasma membrane" node and then on "nucleus" node. |
11) Change the attribute of the path clicking on it with the right mouse button. |
12) Set the path attribute as "<4" (we want a path with length <4). |
13) Click on "Pass to NetMatch" button to upload the query to NetMatch main window. It is also possible to save the query or change its name. The drawing tool window can be closed or can be left opened for other modifications. |
14) Make sure from the Query Properties box the new query (QE-unnamed_1) is selected. |
15) Make sure from the Network Properties box "Yeast Network (galfiltered.gml)" is selected. |
16) Select from the Network Node Attribute menu the "GO Cellular Component" attribute. |
17) Click the "Go" button to start the matching. |
18) The result is showed in the upper left panel. By clicking on a match, the corresponding nodes and edges will be highlighted in the Cytoscape main window. |