Predicting Host-Pathogen Gene Interaction Networks

Question

[a1ultima]

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?

[Sean Davis]

Are your "genomes" actually transcriptomes, or are they truly DNA?

[a1ultima]

They are fully assembled genomes, coding and non coding dna

Answer 1

[Sean Davis]

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.

[liupfskygre]

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!