Dear all,
We now have a collection of transcripts at hand. We would like to investigate some particular ones, which are ion/water channel related. How to perform this? Could anybody point out how to find the annotated genes those are ion/water channel related? If there are some places particularly for fish, that would be perfect. Thanks.
Step 1:
Go to the Gene Ontology website. Identify those Gene Ontology (GO) terms that describe what you are interested in, e.g. ion channel activity and water channel activity.
Step 2:
Go to Ensembl BioMart. Use the GO terms you found in Step 1 to filter out the genes that have been annotated with these terms for your species of interest.
How to work with BioMart is explained in this YouTube video and this Youku video.
If you have any questions regarding Ensembl BioMart, these can be directed to helpdesk@ensembl.org.
Hope this helps.
From my personal experience re-annotating genes using a domain identification algorithm gives additional clarity to your results.It will also help you to quantify your gene-function association. This will be an added advantage because you are looking at genes involved in specific function.
I would try the following steps to find a solution for your problem
Select your protein domain related ion channel activity or aquaporins from Pfam
Download corresponding hmm model and search against your protein sequence (you can derive this from your transcripts or use Ensembl) using HMMER
Rank your proteins based on e-value and coverage assigned by HMMER
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version 2.3.6
if you have the transcripts, why not blast them?
If you can get GO Ids you can look at functional annotation or just look them up in Uniprot. You could also use Pfam's online tool to scan for domains.