Question: Calculating Expression Conservation Score Between Two Gene Co-Expression Networks
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gravatar for reddy.dhivyaa
5.6 years ago by
reddy.dhivyaa80 wrote:

Suppose these two matrices

  set.seed(1) 
  x <- matrix(rnorm(1000), nrow=100, ncol=10)
  y <- matrix(rnorm(1000), nrow=100, ncol=10)

represent the genes (as rows) and genotypes (as columns) for two species.

How to construct a gene co-expression network (by calculating the among genotypes correlation for every pair of genes within each species and the correlations are the edges of the network) . So in total there will be two networks A and B.

Is there any R package to do this and then calculate the expression conservation score (EC score) of each gene in the two gene co-expression networks.

By calculating this EC score for each gene, I assume we would be able to measure the degree of similarity between a candidate's gene neighbours in network "A" and same gene's neighbour in network "B".

R network • 2.4k views
ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by reddy.dhivyaa80
1
gravatar for reddy.dhivyaa
5.6 years ago by
reddy.dhivyaa80 wrote:

I would like to answer my own question as this way of network comparison is very easy.

Considering two species A and B, firstly the gene co-expression network of A and B are determined separately.

Followed by which the expression conservation score is calculated for these two networks which is nothing but correlation of correlations.

For more details I would recommend reading this paper by Dutilh et al, 2006. A global definition of expression content is conserved between orthologs, but does not correlate with sequence conservation.

ADD COMMENTlink written 5.6 years ago by reddy.dhivyaa80
2

If you are interested in gene co-expression network construction and related field, I would recommend to go through the publications of Korbinian Strimmer and his group.

ADD REPLYlink written 5.6 years ago by Sudeep1.6k
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