0
$\begingroup$

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?

Improve this question
$\endgroup$
2
  • $\begingroup$ You must work in Python? Is this a homework assignment? $\endgroup$
    – benn
    Nov 30, 2018 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, 2018 at 11:19

1 Answer 1

Reset to default
1
$\begingroup$

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

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.