Question: How to construct co-expression network with correlation matrix?
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gravatar for MatthewP
11 months ago by
MatthewP740
China
MatthewP740 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 • 429 views
ADD COMMENTlink modified 11 months ago by Arindam Ghosh300 • written 11 months ago by MatthewP740
1
gravatar for Arindam Ghosh
11 months ago by
Arindam Ghosh300
India
Arindam Ghosh300 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 11 months ago by Arindam Ghosh300
1
gravatar for Clément Frainay
11 months 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 11 months ago • written 11 months 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 11 months ago by MatthewP740

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 11 months ago • written 11 months ago by Clément Frainay50

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

ADD REPLYlink written 11 months ago by MatthewP740

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 11 months ago by Kevin Blighe65k
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