how to filter genes in significant module?

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modarzi ▴ 10

@modarzi-16296

Last seen 3.5 years ago

Hi,

I used WGCNA for finding modules. I found 9 modules: turquoise(1501), red(173), pink(41), magenta(36), grey(6), green(446), brown(348), blue(382),black(67). Based on Univariate Cox Model just turquoise is significance. The number of 1501 genes in turquoise module is high and I have to filter more for Gene Enrichment Analysis (GEA) and finding significant pathway. So, how can I decrease the number of genes in turquoise module? Generally, is it reasonable that I run a new clustering between turquoise module? I appreciate if anybody shares his/her comment with me.

RNA WGCNA filter • 1.3k views

ADD COMMENT • link 4.8 years ago modarzi ▴ 10

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Hi Modarzi,

You could run a Gene Enrichment Analysis on modules without filtering, and then focus on the hub of the module i.e., the genes with the highest intramodular connectivity. The hub could includes genes that are known to be involved in that specific pathway.

ADD REPLY • link 4.8 years ago andres.firrincieli ▴ 50

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