Question

Cystoscope network visualization

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Entering edit mode

3.1 years ago

1961012 ▴ 20

I am a beginner in Network analysis and i am facing two major issues in my analysis:

1-I used STRING for protein-protein interaction analysis of my DEGs and I got a huge network even if I take the highest confidence edges for upregulated genes only using String. is there any application in Cytoscape to visualize such a network or filter the nodes to identify hub proteins?

enter image description here

2- I did the Network analysis (NetworkAnalyzer) in cytoscape i got different id for my proteins from those i used as input for STRING analysis. How can I convert the ids and identify my proteins?

string input:

enter image description here

Cytoscape:NetworkAnalyzer (edge table) output:

enter image description here

Thank you in advance!

STRING Ctopscape • 863 views

ADD COMMENT • link updated 3.1 years ago by tothepoint ▴ 800 • written 3.1 years ago by 1961012 ▴ 20

score 1 · Answer 1 · 2021-04-02

1

Entering edit mode

3.1 years ago

tothepoint ▴ 800

MCODE plugin to identify hub genes.

ADD COMMENT • link 3.1 years ago by tothepoint ▴ 800