Predicting Host-Pathogen Gene Interaction Networks
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10.5 years ago
a1ultima ▴ 840

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?

genomics interaction network • 2.9k views
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Are your "genomes" actually transcriptomes, or are they truly DNA?

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They are fully assembled genomes, coding and non coding dna

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10.5 years ago

Gene/gene interactions and gene regulatory networks are largely inferred from gene expression profiling; I do not know of a way to do that from DNA. You may be able to infer some functionality based on DNA sequence and perhaps even about gene-gene interactions based on interactions in other species, but I don't think that is what you are asking.

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Do you have some methods in mind on how to infer gene/gene interactions from gene expression profiling? I have a co-culture system and expression profiling had been done. Now I want to do similar work, thanks!

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