NetMatch by Example
Find all three-chain motifs in galfiltered.sif network where the genes are all significantly differentially expressed (Gal1RGsig < 0.01)
1) Load GalFiltered.sif file from Cytoscape File menu (it is in sampleData directory). |
2) Load gene expression attributes "galExpData.pvals" file from Cytoscape File menu (it is in sampleData directory). |
3) Run NetMatch. |
4) Select drawing tool. |
5) Select "Three chain loop" from Motif Panel clicking on it with left mouse button. |
6) Add The Three Chain on drawing canvas (clicking with the left mouse button). |
7) Change the attribute of the first node clicking on it with the right mouse button. |
8) Set the attribute as "<0.01" (all nodes in the network having a value in the specified attribute <0.01 will match). |
9) In the same way, change the attributes of the remaining nodes to "<0.01". |
10) Click on the Pass to NetMatch button in order to upload the query to NetMatch main window. It is also possible to save the query or change its name. The drawing tool main windows can be closed or can be left opened for other modifications. |
11) Make sure from the Query Properties box the new query (QE-unnamed_1) is selected. |
12) Make sure from the Network Properties box "Galfiltered.sif" is selected. |
13) Select from the Network Node Attribute menu the "gal1RGsig" attribute. |
14) Click the "Go" button to start the matching. |
15) 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. |