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Editor 鈥� Barbara Kramarz
Blood-brain barrier annotation progress and ontology revisions
Mila and Barbara continue to work on GO annotation of the听blood-brain barrier (BBB) proteins, reviewed by听, and listed on our听webpage. To date, Mila has curated 24 endothelial junction proteins, resulting in over 300 annotations, and 10 BBB 鈥榬eceptor-mediated transport鈥� proteins, resulting in over 150 annotations. Barbara has contributed over 250 annotations for 22听additional BBB transport proteins. In total,听听projects have so far resulted in 8961 annotations for 1410 gene products (data from QuickGO, accessed 25th听Nov 2019). Additionally, Mila鈥檚 work on endothelial junctions led her to identify and investigate out-of-date information about 鈥榗ell-cell adherens鈥�-related GO terms. As a听result, Barbara has also been revising the cell junction ontology (e.g. GH听issues听,听,听) and coordinating related annotation reviews (e.g. GH issues听,听,听-) to ensure the information in GO is accurate and up to date. We thank Helen Attrill from听听for her help with these revisions.
New microRNA annotation projects
, our last year鈥檚 MSc project student who听听a distinction and joint top marks in the Genetics of Human Disease MSc course, has听听and is annotating microRNAs (miRs) that regulate the expression of interleukins. This 4-month project, funded from the Functional Gene Annotation group鈥檚 discretionary funds, encompasses the curation of both cardiovascular and neurological processes, and, therefore, her annotations will be attributed to either BHF-UCL or ARUK-UCL. The list of the prioritised interleukin targets can be viewed on our听webpage.
, an intercalated BSc (iBSc) medical student, is going to continue GO annotation of miRs that regulate angiogenesis, an听area previously听curated听产测 . After curation of these miRs Marios will integrate annotation data from both projects to create an angiogenesis miR-mRNA interaction network.
Revision of transcription factor ontology
Following continued GREEKC discussions and a recent meeting in Sarajevo (), the revision of the听鈥楧NA-binding transcription factor鈥� ontology is also leading to a revision of the list of proteins associated with the GO term听听DNA-binding transcription factor activity听(and child terms), which Ruth is contributing to. With almost 5000 annotations associated with over 1000 human proteins, checking the accuracy of these is a challenging task.
Meetings attended
September:听Barbara gave a听听about GO and functional analysis tools at the Qatar University Laboratory Animal Research Center (), Doha; Ruth gave a听presentation听and presented a听poster听about GO annotation of miRs at the听听Conference听at the Wellcome Genome Campus,听Hinxton;听Shirin presented a听poster听about GO curation of miRs in Alzheimer鈥檚 disease at the听听in London.听
October:听Ruth participated in discussions on ontology and annotation revisions at the听听in Berkeley, California, and gave a听presentation at the GO听听entitled:听Interpreting听microRNA听networks with GO;听Shirin presented a听poster听about GO annotation of cardiovascular processes at the听听in London.听
November:听Ruth participated in discussions about annotation of transcription factors at the听听Gene听Regulation Ensemble Effort for the Knowledge Commons听in Sarajevo and gave a presentation about GO curation of miRs and participated in discussions on听听data integration and usability at the听听at the Wellcome Genome Campus, Hinxton.
Recent Publications
Panni S, Lovering RC, Porras P, Orchard S.听Non-coding RNA regulatory networks. Biochim Biophys Acta Gene Regul Mech. 2019 Sep 4:194417. PMID:.
Kramarz B and Lovering RC.听Gene Ontology: A Resource for Analysis and Interpretation of Alzheimer鈥檚 Disease Data. In Wisniewski, T (ed),听听(Chapter听2, pp. 23-36). November 21, 2019.听Codon Publications. DOI:听