How can I calculate and compare intra-cluster correlation for each GO term and pathway?

I want for all the genes, which belong to the same GO-term, calculate a similarity score. Each GO term can be considered as a cluster.

How do I calculate correlation of the time series trajectories for a group consisting of more than 2 genes? In other words, how can I calculate the correlation within a gene cluster?

Which clustering algorithm should I use to infer gene function from time series trajectory similarities?

Please provide long preferentially to Python code. I am especially interested in yeast data.

  • $\begingroup$ Are you aware of WGCNA? I don't know if it is exactly what you are describing, but it finds networks for correlating genes. $\endgroup$ – benn Feb 1 '18 at 9:02
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    $\begingroup$ What kind of similarity score are you looking for? One based on gene expression or pathways or other data you have? What is your attempt to calculate correlation of a group through time? Which methods have you tried/found/looked for? I am not aware that exists methods for inferring gene functions from time series: Where did you come up with that idea? Could you provide a reference? $\endgroup$ – llrs Feb 1 '18 at 9:53
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    $\begingroup$ You mention time series? What time series would this be? Times of what? And what GO? Do you mean biological function? What kind of similarities are you expecting between the proteins? Please edit your question and clarify your objective. $\endgroup$ – terdon Feb 1 '18 at 10:02
  • $\begingroup$ @Thomas Please add more information to the question with an edit, that way we might be able to help you $\endgroup$ – llrs Feb 2 '18 at 9:42

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