Entering edit mode
7.4 years ago
miglanivarnika.26
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20
I am using Cytoscape to build a network which is a union of three or four databases. I want all the interactions seen in the network to be present in a separate file say gene 1 is connected to gene 2 and gene 5 so I want the data as follow:
gene 1 gene 2
gene 1 gene 5
Please help me out with the same. What should I do?Is there a way to do so in cytoscape or I should opt for some other option. if yes, then please let me know the other option.
Thank you for your reply, But I am getting Access is Denied
You need to give more information. "Access denied" doesn't mean anything to me. Is it a Windows message ? If so, maybe it means you're not allowed to write the file in the directory you've selected. I don't use Windows so this is just a guess.
Your guess was right. I have done that. Thank you. can you please tell me the difference between shared name and Human readable name. I am getting shared name I guess.. Is there any setting where I can get the Human readable form, and also what is EBI-6345887. The output I am getting in my SIF file is as follows. Please explain its meaning. "Q07979 EBI-6345887 P40350"
I never got the difference between the name and shared name columns in Cytoscape. The are always identical for my graphs. I am not sure what you mean by human readable form but I think you mean either gene/protein name or gene symbol. Cytoscape doesn't do ID conversion (or maybe there's a plugin for this) so either import your graphs with the desired identifiers or do the conversion once you've exported the graph. The SIF format is: interactor A, interaction_type, interactor B, separated by some white space. EBI-6345887 is an interaction ID from the IntAct database, the other identifiers are UniProt accession numbers. You can also export data seen in the table panel to a csv file using File > Export > Table. After that, you can just process the files with a script to reorganize the data as you need them.
Ohkk, Thank you so much for your answer. It really helped.
What does the graph tell us? Like which of them are proteins, which of them are genes etc. Please acquaint me with this. I am new to usage of cytoscape, rather I am new to the field and I have not got any tutorials or documentation, that could be a benefit.
I would suggest you look for someone to teach/mentor you or find some introductory classes close to you. Failing this, there are plenty of tutorials and introduction to bioinformatics online. See this post for a start. You could also post a new question asking for more specific recommendations.