Tripartite Network Construction
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23 months ago
20180416 ▴ 30

Hello All, Does anyone know how to make tripartite network using cystoscope.I have gene-gene network and drug-gene network. I want to integrated these two networks. Please anyone help me. if i am doing something wrong please let me know as I am new to this (bioinformatics) field.

Thank you in Advance Mohita

gene • 569 views
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Did you encounter any problem? What did you try so far?

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Did you manage to merge the two networks? Do you have given the nodes attributes that indicate whether they represent genes or drugs? If you have done so, you can use a cytoscape filter to select all drugs or all genes and pull them out. And then apply a layout on a subset of nodes (only genes or only drugs) by selecting them with the mouse first.

What do you actually mean by tripartite? What should go into each of the layers?

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Could you define what the contents of the three parts of the network should be, please? Is it 1) drugs, 2) genes with direct links to drugs, 3) genes that do not link to drugs but do link to members of 2. Is it just a visual representation of the tripartite-ness of the network that you want, or do you want some run some analysis algorithm that will prove the tripartite-ness?

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i just want visual representation of the tripartite-ness of the network

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21 months ago
gabt ▴ 110

according to your last comment, you just need a visual representation of the network. There are many ways to achieve this goal but Cytoscape can be the easiest way to go.

First problem: which format is your network? Do you have a file with two columns, where each row represent an interaction? We need something like that, in order to load the network with Cytoscape. Maybe you have a csv files containing at least these two columns and that is ok too. Look into Cytoscape docs to understand how to load a network.

Once the net is loaded into the software, you can use the node table of your network to create a new column called, for instance, "typeOfNode" which will contain the category of each node, i.e. a label. If you had a csv table, it might be the case that such column is already there. If not you have to create it from the table panel, and then manually enter all the categories for all your nodes.

Once you have such column, simply navigate into the Control panel to the Style tab. Here you will find graphical options for nodes, edges and networks (see the tabs at the bottom of the panel). Stick to the nodes tab, and here find Fill Color. Open it and select the column you just decided to use to label your nodes. Then, since you have a tripartite network, three labels should appear and you can select a colour for each one. It's done: you nodes are now coloured accordingly to their label.

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