I am looking for input on ways to compare gene expression profiles between species. The scenario I am thinking of is:
- I have a set of phenotypes in species A, and associated gene expression profiles.
- Now I obtain a gene expression profile for species B.
- Which phenotype in A looks most like the gene expression profile measured for species B?
For example, let's say we knock out a mouse gene and get a gene expression profile which is perturbed relative to the wild type. Which human disease looks most like this knock-out phenotype, based on gene expression?
I suppose this could be done on the gene level (by mapping genes to orthologs), on the pathway level (by assessing which pathways have been perturbed in each case), or on other levels of abstraction. Any success stories out there?
May be I can suggest you something, tell me what you have, microarray or RNA-seq?
RNA-seq in this case, but I don't exclude suggestions or previous work based on microarrays!
I have written my answer, but I think that your question is hot and should be thoroughly discussed on this forum, I am looking forward to have more suggestions/improvements/comments/criticisms