Dear experts, I want to make a network diagram for metabolites and genes based on PCC (Pearson Correlation Coefficient) value. Further, I also want to use the FPKM values of each gene to express their expression level in a network. There are 10 metabolites and each metabolite is associated with 5-10 genes. I want to make a network for all metabolites and genes altogether. Please guide me on how I can arrange my input file to draw a network in Cytoscape?
Please find the attachment for your consideration.
Thanks.
Hi,
Have you looked at the Cytoscape Youtube videos- huge resources available to learn it by self. They have lots of plugins too.
Its all about configuring the .csv/ input files correctly (variables and their relationships-like your PCC) into cytoscape but all after watching the videos. Expression levels (FPKM)/ abundance can be added later on too.
Your challenge is very easy, just that you need to have some patience, and go through those videos and it by yourself and lots of manuals here and there too.
This is one of the best videos that has helped me earlier: https://www.youtube.com/watch?v=qJTp8AUpdFE but then there are 100s to follow and do cool works/ visualization: https://www.youtube.com/results?search_query=cytoscape
Need time and patience to do it yourself or connect with the experts to let them do it for you on a collaborative fashion! : )
Thanks,
Biswa
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