How To Handle Microarray Data In Cytoscape

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10.7 years ago

avi4you ▴ 20

i am a begiener, and doing my masters degree research work,, i am currently working on gene expression data for avian influenza in ducks with the help of microarray. i want to make a network of genes which are present in my data for downstream analysis.but i am struck as i dont know how to make network from a microarray gene expression data. i have data in the format :

probe name comman name fold change p valuE

Duck_1254 MYBPC1 2.636 0.01 . .

.

AND SO ON

Please suggest me how to proceed ? and can this be done with the help of cytoscape.

cytoscape microarray • 4.3k views

ADD COMMENT • link updated 10.6 years ago by Biostar 20 • written 10.7 years ago by avi4you ▴ 20

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There are many different kinds of network. What kind do you want to make? Sounds like co-expression?

ADD REPLY • link 10.7 years ago by Neilfws 49k

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yes sir co expression network, please guide me

ADD REPLY • link 10.7 years ago by avi4you ▴ 20

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You might try WGCNA, then.

ADD REPLY • link 10.7 years ago by Devon Ryan 105k

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might want to check out CORNET https://cornet.psb.ugent.be/main/tool

ADD REPLY • link 10.7 years ago by dcolinmorgan ▴ 100

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