Hello,

i have datasets derived from microarray experiments and I want to reconstruct gene coexpression networks.I know i have to compute the Pearson Correlation coefficient at first. Are there different methods to continue the analysis and reconstruct the networks? Can you recommend software?

Another comment on Pearson Correlation Coefficient. Be very cautious with this metric as it is known to have serious issues with over- and under-estimating correlation because of the influence of small numbers of outliers. It might be a better idea to use Spearman correlation or Euclidian distance.

Speaking of Pearson Correlation Coefficient in relation to gene coexpression, you might also want to check out Mixed-Model Coexpression that was introduced in this publication: "Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity". An R implementation is available on their web-site: http://genetics.cs.ucla.edu/mmc/