Gene networking in transcriptome data

Question

[ashokkumartherock]

I have defense related gene from mango transcriptome. Mango genome is not published yet. Is it possible to study gene networking study on these gene

Answer 1

[Jean-Karim Heriche]

The usual approach when dealing with an organism for which little data is available is to transfer gene product properties by orthology i.e. build a mango gene network by assuming that two mango genes are linked if their orthologs in some other more studied species are linked.

[ashokkumartherock]

Thank you so much sir for your valueable suggestion

[ashokkumartherock]

sir in the STRING software the closest species genome information is not added, but their genome is published. So is there any offline software to perform the gene networking studies or is there any procedure to add genome information in string software manually.

[Jean-Karim Heriche]

It's not because the genome of an organism is published that there is an abundance of data on proteins from this organism. Unless the genes you're interested in are only present within a specific clade, you don't need the closest species. Since most data is about human and model organisms proteins, I would find out the model organisms genes that are orthologous to your genes of interest.