How to read WGCNA edge file output to find the hub genes_ GO ontology
Entering edit mode
8 weeks ago
synat.keam ▴ 30

Dear Seniors and members,

I am getting close to finish my analysis soon, but I would like to ask two more questions. Hope you do not mind me.

Question 1

I have WGCNA edge file for cytoscape. I have sorted the weight column in decreasing order so genes with mamixum weight will be at the top. Are top 1, 2, 3, or 4 hubgene? or is there any criteria to identifying hub genes from edge file using weight column because I would like to visualize hub genes in cytoscape.

There are columns from (fromAltName to fromAltName) and (fromNode to Node). Which column is used to name the hub genes? Hope you get what I meant? I have attached the output here.

enter image description here

Question 2

I have one module I like to perform gene Ontology. I used gene Ontology website to perform over representation analysis. First I pasted my genelist in box at top right hand side (picture attached) and then selected category of interest then organism and clicked launch.

enter image description here

Finally I got th result page as shown in attached. I am wondering whether this is the right approach to do? I understand I have ask many quesitons recently. Hope you do not mind me. Looking forward to hearing from all seniors soon.

enter image description here

Kind Regards,


WGCNA hubgene • 119 views

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