**290**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!

**200**• written 28 days ago by MatthewP •

**290**

Question: How to construct co-expression network with correlation matrix?

0

MatthewP • **290** 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!

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modified 27 days ago
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Arindam Ghosh • **200**
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28 days ago by
MatthewP • **290**

1

Arindam Ghosh • **200** 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.

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Clément Frainay • **50** 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

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.

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

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

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