Cytoscape tutorial: How to add gene expression data to an interaction network
Автор: bioZone
Загружено: 2019-07-19
Просмотров: 43396
Describes how to:
1. Load an interaction network on cytoscape from a file (uses bioGRID)
2. Filter nodes by species and create a sub-network from filtered nodes
3. Add your gene expression data to the network in the form of a table
4. Change the color of the nodes to represent the changes in gene expression
5. Search for a specific node in the network and create a sub-network from all nodes that interact with this node
6. Change the layout of the network
7. Save the network as an image
8. Save the node or edge table as a .csv file
*This video was edited to remove the wait time while cytoscape is loading. Many of the steps take a long time and this in real time took a lot longer than 9 minutes.
0:00 download interaction data from bioGRID
1:10 load an interaction network on cytoscape from a file
2:02 filter nodes by attribute
2:50 create sub-network
3:10 add gene expression table
3:56 change color of nodes using gene expression
5:13 search for a node & create a sub-network from interacting nodes
6:32 remove duplicate edges
7:10 change the layout of the network
7:46 save the network as an image
7:59 save the node or edge table as a .csv file
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