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well, I'm new to Bio. what I'm going to do is create a network/graph of a dataset related to the genes I think. here's the sample of the nodes dataset with CSV format named lung-nodes : enter image description here

and this is a sample of edges I think with trrust name : enter image description here

these data are stored in two separate file

what I must do is create a graph(network) of these nodes and edges by Python and a visualization library like networkX, but I do not how. I must make a relation between these to the dataset by creating a graph of them can you help me out?

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  • $\begingroup$ You must work in Python? Is this a homework assignment? $\endgroup$ – benn Nov 30 '18 at 10:54
  • $\begingroup$ @benn, yes it is. I am not familiar so much with gene and protein properties. I already create a graph from social network dataset but they weren't like this. they had just two column in a single file. but right now i got two separate CSV file which contains bio info which i must create a graph of them. i think R studio could make it easier $\endgroup$ – Mohammad Heydari Nov 30 '18 at 11:19
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As far as I understand, it seems that the first table you provided contains biological/experimental information related to your genes, i.e. the nodes of the network you will build. The second table is the one you need to build the network: each line is an edge. You can use it as input and build the network using the IGraph library which works for both Python (as you requested) or R (as you suggested as an alternative).

Most probably, but I can't say for sure, the first table was just a dataset from which you (or someone for you) recovered a list of nodes that where then submitted to a database, i.e. String, commonly used to recover information related to the interactions between your nodes, i.e. genes. Once you have this info (in the second table) you can build the network!

edit:

if you're not familiar with IGraph, you can have a look at this question describing how to obtain an IGraph graph from a csv file or this other one which uses a different csv file format to build a graph

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