How To Find All Genes In A Biological System ?

Question

[Khader Shameer]

I need to get the list of all genes associated with various biological system (for example 'circulatory system'). AFAIK, molecular biology databases are not annotated with information about 'biological systems' or is there any database that I am missing ? What could be the best way to find all genes of a particular system ?

[Giovanni M Dall'Olio]

what does it mean that a gene is associated with a biological system? Is that it is expressed in these organs? Or that it is required for those organs to work? Can you explain it better, please?

[Khader Shameer]

I define them as genes expressed in the organs of a given biological system.

Answer 1

[Pierre Lindenbaum]

Have a look at the Cardiovascular Gene Ontology Annotation Initiative

Update: see also GeneOntology.

[Khader Shameer]

Thanks Pierre, I am using CVGO as my basic dataset. The GO term "Circulation" is new to me. But Here I need to compare genes between the systems and these two resources are confined to circulatory system or it's subsets.

[Pierre Lindenbaum]

I'm interested by this question because soon, I'll have to find a collection of genes involved in the Cardiac functions.

[Jarretinha]

Wow! CGOA identified 4000 genes related to cardiovascular system. For a species with at best 30000 different genes, I think that's way to much!

Answer 2

[Jarretinha]

Adding to Pierre's idea, it's necessary to choose a attribute set that define circulatory system or it's synonymous. Then you just need to look up on a specific ontology for genes with the desired degree of overlap with this set. The hard part is to gather a good set! You can look for attributes of the cardiovascular sytem in the Open Biological and Biomedical Ontologies that includes GO and many more. Another good place is the National Center for Biomedical Ontology.

In this places you can find a lot clinical, structural, anatomical attributes of the cardiovascular system. With this set in hand you can fish genes inside GO or even in GenBank by using literature fields.

That's it for now.

[Khader Shameer]

Thanks Jarretinha: Going via GO is an interesting option. But for most of these ontologies, inter-ontology mappings are not available and manual curation may take long time and efforts. I think it will be a separate project on its own. I will talk to some of the NCBO folks and see.