Hello everyone
I am doing a research on olive flounder and I got a set of genes which are influenced by microrna. I want to do a gene ontology for this set of genes and I want to do also a pathway analysis using DAVID, but I didn't find the species of interest.
For gene ontology I checked the gene ontology website but also I didn't find olive flounder.
So my question is; how can I do the gene ontology, and if possible can anyone show me the protocol and software used for doing it?
Hi Adham,
I do not think that you would get any genome data required for pathway analyses on Paralichthys olivaceus (Olive flounder) in general.
There are a few transcriptome data available. Please refer to http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117642 for obtaining the transcriptome if possible and then you can compare your sets.
Hope this helps
Best
Sayak
if your species is not annotated, the quick and dirty functional analysis is blast2go. Thus, you retrieve functional annotation through homology, betting that most genes didn't change their functionality.
https://www.blast2go.com/
May be using Danio rerio (zebrafish) anotations might be the closest way.
http://geneontology.org/page/download-annotations
it is the last one in the table
Hi Adham,
You also could do a molecular phylogeny and find the most similar organism that have annotations on Gene Ontology
thanks a lot for your help. i annotated the mRNA of olive flounder retrieved from NCBI data using blast2Go through the tool interproscan. now i need to compare the mRNA influenced with microRNA the annotated reference. how can i do it ?
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Nucleic Acids
- RNA
- Small RNA
- microRNA