how can I extract group or modules from a huge number of intractions between gene-TF or gene-miRNA

falsafi...@gmail.com

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Nov 24, 2018, 3:06:13 AM11/24/18

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Hi, would you please anyone explain how can I extract group or modules from a huge number of intractions between gene-TF or gene-miRNA? I mean, I have a network with more than 100,000 intractions between TFs and genes or miRNA-genes and it is a big network, I only want nodes with highest number of interactions to reduce the number of interaction to a tenth or a percent.

piet molenaar

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Nov 26, 2018, 7:46:13 AM11/26/18

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Hi,

If you run Tools>NetworkAnalyzer>Network Analysis>Analyze network your network will be annotated with quite some graph parameters. Amongst these is the degree.

Use the Select tab to filter for nodes having a high degree subsequently (more on that here: https://cytoscape.org/cytoscape-tutorials/protocols/filtering-by-selection/#/)

Hope this helps

Piet

On Sat, Nov 24, 2018 at 9:06 AM <falsafi...@gmail.com> wrote:

Hi, would you please anyone explain how can I extract group or modules from a huge number of intractions between gene-TF or gene-miRNA? I mean, I have a network with more than 100,000 intractions between TFs and genes or miRNA-genes and it is a big network, I only want nodes with highest number of interactions to reduce the number of interaction to a tenth or a percent.

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Amsterdam University Medical Centers
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

falsafi.raziuni

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Nov 26, 2018, 9:08:14 AM11/26/18

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Thanks Piet for your helpful comment.

Would you explain is there any way to filter out network base on a combination of degree and other centrality paramerters, like, betweenness, radiality and so on?

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