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

Suppose these two matrices

  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
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

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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