I found several lncRNAs and also identified the microRNAs and genes associated with those lncRNAs. How can I draw overlapping between microRNAs interaction with long non coding RNA?
Furthermore, I got the txt file of microRNAs associated with an lncRNA, and I did IMPORT it to Cytoscape, but unfortunately it could not draw the interaction network (micro-RNAs and lncRNA) for me. How do I draw networks and nodes using the TXT and EXCELL files using the Cytoscape program?
Best wishes,
Mohsen
Hi Mohsen，
I cannot understand your first question, but for the second one, it's quite easy to construct network with your TXT or EXCELL files using Cytoscape.
To construct a network, you first should create a TXT or EXCELL files with at least two columns, i.e, two nodes interacting with each other, separated with tab, coma, semicoma, or other separators. For the third column, it could be edge attribute, e.g., the edge weight. For your case, you wanna draw a microRNA-lncRNA network. For example, you have 30 microRNAs associated with a lncRNA. So the number of interactions should be 30. That means there should be 30 rows in your file, with 2 columns per row - a microRNA & the lncRNA. Finally, the option button "import network from file" should be selected & in the pop-up window select the 1st column as source node, the 2nd column as target node. Then click OK to construct the mRNA-lncRNA network.
Hope this answer could help you a little bit. @Mohsen Sheykhhasan
Best,
Yanshi
Hi Mohsen，
I cannot understand your first question, but for the second one, it's quite easy to construct network with your TXT or EXCELL files using Cytoscape.
To construct a network, you first should create a TXT or EXCELL files with at least two columns, i.e, two nodes interacting with each other, separated with tab, coma, semicoma, or other separators. For the third column, it could be edge attribute, e.g., the edge weight. For your case, you wanna draw a microRNA-lncRNA network. For example, you have 30 microRNAs associated with a lncRNA. So the number of interactions should be 30. That means there should be 30 rows in your file, with 2 columns per row - a microRNA & the lncRNA. Finally, the option button "import network from file" should be selected & in the pop-up window select the 1st column as source node, the 2nd column as target node. Then click OK to construct the mRNA-lncRNA network.
Hope this answer could help you a little bit. @Mohsen Sheykhhasan
Best,
Yanshi
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