cmungall
commented
3 years ago Hello @pmaye, thanks for using our resource!
Can I ask how you are using our resource to analyze your differentially expressed genes? Are you using the panther enrichment tool, or are you looking at gene annotations on a gene-by-gene basis? Is this in mouse?
It sounds like you are expecting to see more skeletal annotations for your genes of interest. Sorry you are not finding the results you are expecting. Do you have some specific examples?
It may be worth bearing in mind GO is primarily a resource for understanding the normal wild-type function of genes, with an emphasis on cellular biology. Annotations to MP describe effects of mutations. Parts of GO parallel MP (particularly development terms) and are coordinated - but in general we would not adopt MP terms in wholesale as it is intended for a different purposes. However, there may be gaps the MP can help fill and if you have specific suggestions we can look at them.
We do in fact work closely with the developers of MP and the annotators, and annotations to phenotype ontologies are sometimes transferred to analogous GO annotations via the IMP evidence code.
You may also be interested in resources for analyzing RNAseq data that leverage complementary ontology annotations to GO
- TopAnat https://bgee.org/?page=top_anat# can be used to see if your gene list is enriched for particular tissues
- ToppGene https://toppgene.cchmc.org/ can use a variety of other ontology systems including I think MP
However, if you are interested in the function of the gene then GO is the main resource, and we would like to make it as complete as possible in the area of skeletal biology, if you can provide assistance with some specific terms or annotations you would like to see that would help us a lot, thanks!
pgaudet
Many investigators, including myself, have used your website when performing an RNAseq study to understand the role of different differentially expressed genes. The terms associated with skeletal biology are significantly lacking on your website and I was wondering whether you could simply adopt some of the phenotyping tree terms available on the MGI website (http://www.informatics.jax.org/vocab/mp_ontology/MP:0004624) to quickly increase the number of GO terms.