Cytoscape - long list of proteins, very messy result
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7 weeks ago

Hi everyone,

I am mid-way through my university project, and I have run into an issue. I have a long list of around 1000 proteins that I wanted to analyse in STRING, however, my list is too large. I decided to try and utilise Cytoscape (and downloaded the stringApp), but the networks generated are still very messy. I've attached a screenshot: https://i.stack.imgur.com/KUIE4.jpg. Is there any way to improve the presentation of the network by downloading any Cytoscape apps or by tweaking the settings? I am very much a novice when it comes to Cytoscape, even after watching quite a few tutorials online.

Thanks in advance

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Hi, in STRING download section you can access to the multiple filters based on the biological evidence that connects two proteins. For example, you can just select the evidence "PPI" or "coexpression", or "gene neighborhood". Also, if you want to keep all evidences, you can still filter the list of interactions for a cutoff arbitrary score. So what I suggest is to download the interactions and, based on the filters/cutoffs you decide, filter the data. Finally, you import the dataset in cytoscape itself and play with the visualization options.

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Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image or the HTML embed code, not the link to the webpage that has the image embedded (which is what you have used here)

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7 weeks ago
Mensur Dlakic ★ 10k

It would be very difficulty to see individual proteins and their interactions when the number is 1000. In such cases the best you can do is play with different layouts in Cytoscape to get a meaningful global representation. I have made networks with 15000+ proteins in Cytoscape, but those are not meant for looking into individual proteins and their interactions.

Here is an example of all c.1. folds in SCOP and their relationships, which is comparable in number to what you have.

enter image description here

As you were already told above, adjust the stringency of your criteria to get most reliable interactions for your protein(s) of interest, and that should reduce the number of proteins and be easier to visualize. Either way you will have to play with layouts, or else any network will end up looking like a blob in your image.

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5 weeks ago

Thanks, everyone for the help!

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