Building a Network from gene expression data

Question

[1769mkc]

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.

Answer 1

[lessismore]

There could be quite a lot of answers. Of course it depends by your biological questions. How To Build Co-Expression Networks? how to make regulatory network from microarray data Gene regulatory networks from RNA-seq data What data should i use to generate a gene coexpression network?

i found this review quite complete https://www.ncbi.nlm.nih.gov/pubmed/28077403

Answer 2

[Arup Ghosh]

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

[1769mkc]

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