Building a Network from gene expression data
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3.3 years ago
krushnach80 ▴ 910

I have been going through paper mostly of Gene regulatory network , most of the paper starts with a base network which is mostly curated experimentally validated and those data are available in various databases.

But my question is , would it be logical to create a gene regulatory network from RNA seq expression data ,mostly differentially expressed data ,I came across Reactome FI plugin where there is an option to do gene expression analysis but it says microarray data analysis this paper doing something similar...I would like to get some input as well as suggestion about tools and methods that would be helpful in doing so.

RNA-Seq • 3.0k views
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3.3 years ago

Only with the gene expression data, a co-expression network is possible, but not directly gene regulatory networks. Co-expression networks only group the genes having a similar expression pattern that may or may not have any biological meaning. For gene regulatory networks you have to take transcription factors as well as epigenetic elements in the account to get a meaningful insight.

I would suggest you look into the following paper for more insight about gene regulatory network.

http://www.cell.com/cell-systems/abstract/S2405-4712(17)30090-X

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yes co-expression seems spurious I did in wgcna most of them shows which is not intended , yes gene regulatory network is more reasonable as compared to co-expression one's

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