Question: Inferring gene function from homologus genes.
0
gravatar for giuseppe.minardi95
7 days ago by
giuseppe.minardi9510 wrote:

I and my group have two lists of genes (with related gene networks): one from Arabidopsis and one from Vitis Vinifera. Those lists were found by expanding ERF gene network in both organisms starting from expression profiles (therefore we also gene networks for both organisms).

Our goal is to infer V. Vinifera's gene functions using sequences homologies with Arabidopsis genes, but I'm struggling to find a decent pipeline for our task. Are there any pipeline/papers that describe a method to infer gene function using the material that we have?

Our first idea was to cluster Arabidopsis genes and then infer those cluster of Vitis knowing which gene is homologous to which other gene, but we do not know exactly how a gene list can be clustered.

gene genome • 113 views
ADD COMMENTlink modified 6 days ago by natasha.sernova3.3k • written 7 days ago by giuseppe.minardi9510

See figure 2 and table 2 from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001326

It may help.

There are more than 700 articles citing this one above, there should be some updates.

https://journals.plos.org/plosone/article/citation?id=10.1371/journal.pone.0001326

ADD REPLYlink modified 6 days ago • written 6 days ago by natasha.sernova3.3k

What do you mean a pipeline for this?

You can literally just use BLAST of the V. vinifera sequence to find what it's similar too. You'd probably also want to look at Interproscan, and some HMM methods (e.g. hhpred) to identify domains of function within the sequence etc.

If the databases don't contain informative hits though, you have to go in the lab.

ADD REPLYlink written 6 days ago by jrj.healey10k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 690 users visited in the last hour