Question: gene ontology for olive flounder
gravatar for najibveto
5.2 years ago by
Korea, Republic Of
najibveto0 wrote:

hello everyone

i am doing a research on olive flounder and i got a set of gene which 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 specie of interest.

for gene ontology i checked gene ontology website but also i didn't find olive flounder.

so my question how can i do the gene ontology? and if possible to show me the protocol and software used for doing it.

ADD COMMENTlink modified 2.4 years ago by Michael Dondrup48k • written 5.2 years ago by najibveto0

thanks a lot for your answer. but i wanna do GO enrichment analysis to see the biological function of a set of genes. so i don't know how to do it for olive flounder.

ADD REPLYlink written 5.2 years ago by najibveto0
gravatar for Antonio R. Franco
5.2 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

By looking for homology is the only chance you have. Doing a BlastX from the DNA/cDNA sequences you already have

There are some programs already described here in biostars. I personally recommend Blast2Go.

ADD COMMENTlink modified 14 months ago by _r_am32k • written 5.2 years ago by Antonio R. Franco4.5k
gravatar for Michael Dondrup
5.2 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

Your fish is not a model-organism, no genome is published (except mitochondrial) and so there is no ready-to use GO annotation for your data, so you have to do all the work yourself and can't use practical online tools all the way.

See Go In Non-Model Organisms GO enrichment in non-model organism for similar questions

I guess you got annotated transcripts from a TSA, if not you need to specify what other data is available.

  1. Assign GO terms to transcripts (you can use Blast2GO or e.g. run InterProScan)
  2. Do GO-term enrichment analysis using a tool that is suitable for non-model organisms, see Looking for a tool to do GO enrichment analysis with BLAST2GO output(s) and GO enrichment analysis using non model organism
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Michael Dondrup48k

thanks a lot for your help. First I did an experiment of bacterial infection in olive flounder, after that I got the differentially expressed microrna and I did microrna target prediction using Miranda tool. So I got the target genes based on the mRNA from NCBI database for olive flounder. So I wanna do the gene ontology enrichment for the target genes. So for annotation should I use the data from NCBI or should I use it from another database? After that which software should I use for GO enrichment?

ADD REPLYlink modified 14 months ago by _r_am32k • written 5.2 years ago by najibveto0

It might look surprising, but there is no simple way to do this. You need to annotate all mRNA's with GO terms. NCBI mRNA likely doesn't contain GO annotation, if you find another db that's fine, but I don't know any for flounder. You will download all NCBI mRNA's for the organsim and run one of the tools listed under 1. This is because you need a background distribution, you cannot only annotate your genes of interest, and there might be heavy selection bias in the mRNA sequences, depending on how they have been sampled.

This annotation process should produce a GAF file with GO terms for each mRNA. Using this file you can use the tools listed under the links in item 2.

Here are some articles dealing with the same organism and GO, you have to check further if they have submitted their transcripts and GO annotations to genbank.

ADD REPLYlink modified 14 months ago by _r_am32k • written 5.2 years ago by Michael Dondrup48k

Hello thanks a lot for your help. I annotated the reference mRNA using InterProScan under blast2GO and give a text file with genes annotation. I didn't work before with R so I don't know how to use the different file with my genes of interest.

ADD REPLYlink modified 14 months ago by _r_am32k • written 5.2 years ago by najibveto40
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