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Cytoscape

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Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

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Roopesh Singh
Post-doc at Hebrew University of Jerusalem
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Roopesh Singh

Post-doc at Hebrew University of Jerusalem

How do I plot a network plot by performing correlation analysis? Oval 17

Hi,
I need to know how to plot a network plot by performing correlation analysis, with the data I have. it is not the gen/protein sequence data. It is the clinical data from the patients. Any help will be greatly appreciated. Thanking you. Roopesh

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Posted: 3 years ago
ch.shteiger
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If I understand correctly you are referring to two types of corrections:
1. Between each gene & clinical data (e.g. bad prognosis)
2. Among different genes (to generate a network)

So I would recommend that you first calculate the correlation between all genes & the desired clinical attribute (in excel/matlab etc..) and once you have that data you can use Cytoscape to create a network between the genes based on their effects.

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Posted: 3 years ago
Roopesh Singh
Post-doc at Hebrew University of Jerusalem
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Roopesh Singh

Post-doc at Hebrew University of Jerusalem

Thanks ch.shteiger,
I will try as you suggested. To be more precise in my question. I have blood levers of certain cytokines, and I have drug dose given to these patients, and I have the numbers of eosinophils, neutrophils in the blood of these patients. If I do correlations for example in eos% and cytokine levels, I have a significant correlations. so at a time I can do correlation between 2 parameter. But I want to know how these parameters are related to the disease severity, I mean which one affect the most and vice versa... So I think this can be plotted in a network plot attached by lines of different thickness or may be circles of different sizes. I will try as you suggested.

Thanks
Roopesh

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Posted: 3 years ago
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