Question: Building a Network from gene expression data
gravatar for krushnach80
14 months ago by
krushnach80480 wrote:

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 • 1.5k views
ADD COMMENTlink modified 14 months ago by arup1.2k • written 14 months ago by krushnach80480
gravatar for lessismore
14 months ago by
lessismore610 wrote:

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

ADD COMMENTlink written 14 months ago by lessismore610
gravatar for arup
14 months ago by
arup1.2k wrote:

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.

ADD COMMENTlink written 14 months ago by arup1.2k

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

ADD REPLYlink written 14 months ago by krushnach80480
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1727 users visited in the last hour