Conservation of co-expressed genes across transcriptomes
Hello !
I have a set of co-expressed genes (about 100 ) from one species and want to search them across transcriptomes from different genera and species.
I want to infer how well they are connected evolutionary in terms of their conservation and co-expression.
Apart from doing BLAST(or tBLASTn) search in these transcriptomes, what would be other ways to analyze this ? Methods/parameters/pitfalls etc...? Please help !
Many thanks.
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Depending on what transcriptomes these are some of this information may be pre-computed by NCBI, UCSC or Ensembl. Take a look at Homologne.
Looking at plant transcriptomes. Not pre-computed in these DBs.
Then you know what to do as you noted above. Plants obviously add complexity to the analysis because of ploidy etc.