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Background

What we have are:

  • ~20 genome sequences for a host species that come with gene annotations
  • Several sequenced genomes for parasite/pathogens of these hosts

Question

What are the possible ways of predicting gene-to-gene interactions or gene regulatory networks between hosts and parasites?

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About what kind of interactions do you think? Transcription factors from parasites that influence the host? –  Chris Jan 8 at 16:03
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thanks for the question. at the simplest level an interaction would involve binding, e.g. gene A that expresses a transcription factor that represses gene B via binding it's promoter sequence would be considered an interaction between gene A and gene B. –  hello_there_andy Jan 8 at 16:31
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there is no way by which you can predict genetic interactions based on sequence alone.. You need more information such as protein-DNA interactions, expression correlation, protein-protein interaction etc –  WYSIWYG Jan 8 at 20:18
    
exactly! which is why i am asking the question i suppose, you hinted at some ideas there thank you - could you expand on them? –  hello_there_andy Jan 9 at 23:31

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