Question

WGCNA Co-expression

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munirapcu • 0

@munirapcu-12086

Last seen 7.1 years ago

Hello Everyone,

How to use differential expressed genes (DEG) as input data for module detection ?. Because, I am unable to understand proper codes for this experiment.

microarray differential gene expression module • 1.3k views

ADD COMMENT • link updated 7.3 years ago by Peter Langfelder ★ 3.0k • written 7.3 years ago by munirapcu • 0

score 1 · Answer 1 · 2016-12-29

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Peter Langfelder ★ 3.0k

@peter-langfelder-4469

Last seen 23 days ago

United States

Please read WGCNA FAQ, item 2, at

https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html

We don't recommend filtering genes by differential expression.

As for using WGCNA, there are several tutorials at https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html. They will show you how to use the package.

ADD COMMENT • link 7.3 years ago Peter Langfelder ★ 3.0k

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these papers (Identification of hub genes of pneumocyte senescence induced by thoracic irradiation using weighted gene co‑expression network analysis, Integration of Gene Coexpression Network, GO Enrichment Analysis for
Identification Gene Expression Signature of Invasive Bladder Carcinoma) and like other papers they have clearly mentioned that, they have taken DEGs for module detection in WGCNA.

ADD REPLY • link 7.3 years ago munirapcu • 0

score 0 · Answer 2 · 2016-12-30

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Peter Langfelder ★ 3.0k

@peter-langfelder-4469

Last seen 23 days ago

United States

Some people do it despite (or not knowing) our recommendation, perhaps they have good reasons to do so. Still, the general recommendation is not to filter genes by DE.

I suggest you work through the tutorials and run your own analysis along the lines of the tutorial.

ADD COMMENT • link 7.3 years ago Peter Langfelder ★ 3.0k