Question: Merge Networks using Cytoscape
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gravatar for Soltani
4.5 years ago by
Soltani50
Tunisia
Soltani50 wrote:

Hello,

I have Two Regulatory Interaction Networks (RegINs) created from two different databases (miRNAs-Targets interactions) ! I tried to merge the two files to obtain a global network but everytime i lose some important nodes ! Please tell me  How can I merge the two RegIns without losing any node or edge ! Thanks in advance!

ADD COMMENTlink modified 4.3 years ago by Biostar ♦♦ 20 • written 4.5 years ago by Soltani50

Could you please provide some clarification. Are you trying to merge network using build-in Cytoscape functions? Are you storing yout networks in tab-delimited tables (net/nodes/edges) and then import them to Cytoscape?

ADD REPLYlink written 4.5 years ago by mikhail.shugay3.3k

Am trying to combine two Regulatory Interaction Networks files (xgmml files) e.g Tarbase-xgmml file  with Mirecords -xgmml file to obtain a global network that contain all miRNAs-Targets interactions from both databases.

ADD REPLYlink written 4.5 years ago by Soltani50

Ah ok. As far as I understand it could be not quite possible (https://groups.google.com/forum/#!msg/cytoscapeweb-discuss/A-7IaZVWOnk/0xWARv53l5sJ), e.g. XGMML contains node coordinates, which are not straightforward to merge. Anyways, you have an option to export to tab-delimited table from Cytoscape (loosing some info), do merge for them, import them back and perform layout/setup VizMapper.

ADD REPLYlink written 4.5 years ago by mikhail.shugay3.3k
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