Hi everyone!
I annotated thousands of genes of a given organism using GO biological process terms and I would like to map these terms and/or genes to specific tissues/organs. For example, gene A was annotated to the term "signal transduction" and I would like to find to which tissue/organ this term would be mapped.
From my understanding, Gene Ontology terms are generally not tissue or organ specific. Terms such as "signal transduction' , "membranes and envelopes", or "cell cycle" are found in all cells and tissues. There may be some lineage specific terms, especially for developing tissues, but for the most part, I think the GO terms apply to all cells and tissues.
Ontology itself could not tell you any information for specific tissues or organs? Generally, clear connections between them were considered based on ontology statistical analysis combined with dynamic data sets, e.g. RNA-seq
The term 'signal transduction' is of course general and should not be specific to any tissue/organ/cell. But other terms such as "eye photoreceptor cell development", "regulation of hepatocyte proliferation", "positive regulation of skeletal muscle cell proliferation", for example, are undoubtly specific to, respectively, eye, liver and muscle. My question is if there is any tissue/organ/cell ontology linked to Gene Ontology. I've recently found UBERON (uberon.org/), but I'd like to know whether there additional resources like this.
I major in plant bioinformatics and am not really familiar with human or mammalian biology, but I indeed heard of cell tology and tissue ontology here http://www.obofoundry.org/. However, I have no idea about whether these ontologies were assigned to each gene as GO does.
I worked on a couple of databases that might help you find what you're looking for:
TISSUES is a frequently updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. We map all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. We finally visualize these scores on a schematic human body to provide a convenient overview.
http://tissues.jensenlab.org
And we created a similar resource for sub-cellular location of proteins expressed in all kingdoms of life:
http://compartments.jensenlab.org
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