Question: How to construct co-expression network with correlation matrix?
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gravatar for MatthewP
28 days ago by
MatthewP290
China
MatthewP290 wrote:

Hello, I know how to calculate pearson correlation matrix, but don't know how to construct co-expression network from it. Also shall I filter correlation matrix according each P value? Thanks!

rna-seq • 130 views
ADD COMMENTlink modified 27 days ago by Arindam Ghosh200 • written 28 days ago by MatthewP290
1
gravatar for Arindam Ghosh
27 days ago by
Arindam Ghosh200
India
Arindam Ghosh200 wrote:

Refer to Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data. The section 3.12 Calculating Correlation of Gene Expression for Every Pair of Genes explains the steps.

ADD COMMENTlink written 27 days ago by Arindam Ghosh200
1
gravatar for Clément Frainay
27 days ago by
Clément Frainay50 wrote:

I don't know much about co-expression networks, but maybe this can helps you : https://medium.com/@JavierBurroni/visualising-correlations-using-graph-2169c6415427

You can build a network with the igraph library (available python or R), from an adjacency matrix obtained by simply applying a threshold on your correlation matrix.

However you obtain a correlation network, not sure if this is enough to call this a co-expression network

ADD COMMENTlink modified 27 days ago • written 27 days ago by Clément Frainay50

Thanks, Clément Frainay. I know igraph but I have the same confusion with you that is this the co-expression network? Many papers said use pearson correlation to construct such network, but no detail how to perform. As for me, I want to construct co-expression only for differential expression genes and find hub genes(However I don't know such analysis pipeline is suitable or not). I know we can construct networks and find hub genes use gene list and string, but that is PPI, not co-expression network.

ADD REPLYlink written 27 days ago by MatthewP290

Ok. If you want to compare two conditions, maybe you want to look at differential networks? Not sure if it helps, but here is an example with detailed computation procedure : https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-95

ADD REPLYlink modified 27 days ago • written 27 days ago by Clément Frainay50

Ok, I think this post is helpful for me. Thanks again!

ADD REPLYlink written 27 days ago by MatthewP290

Hey Matthew, you mentioned my tutorial. Please let me know if you have issues in running it. I believe I show how to determine hub genes in the tutorial.

ADD REPLYlink written 27 days ago by Kevin Blighe51k
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