I have 72 proteins which have been changed after cell treatment. I would like illustrate a network, based on this genes. I wanted to use cytoscape (v 3.7.1). but I do not know how and in which format to load these 72 proteins in cytoscape to get network connection. I have tried string for them and found some connection. I donot know how to do that in cytoscape. please can someone give me detailed step by step to follow.
Hi Ranjan, there are at least 3 ways to do what you want to do.
1. From STRING database you can download your network in a tab-separated txt format (in the export tab), and then load it as a network on cytoscape.
2. You can also manually build your network in an excel file, as your network comprises a small number of proteins/interactions. You should have at least 3 columns which you can name as "Source", "Target" and "Interaction". In Source you put the source protein, in target you will put the target protein and in interaction you will put a string that represents the interaction (for example "activation" or "inhibition". You will load it on cytoscape, select which is the source and the target nodes, and the interaction. Then you can apply your preferred styles.
3. On Cytoscape you can install the STRING application, which allows you to put a list of proteins and query the STRING database, which will return a protein network directly on Cytoscape for further style editing.
Thanks a lot, sir.
How can I contact you if I am stuck in any step?
Whatsapp no./mail id??
Hi Ranjan
you can do the following steps:
Open Cytoscape
File
Import
Network from Public Databases
Data source: STRING: protein query column of data as like:
ALB
MYC
......
Import
you can analyze the network via tools option
Network Analyzer
Network Analysis.
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