UCL Institute of Cardiovascular Science


December 2019

Editor – Barbara Kramarz

Blood-brain barrier annotation progress and ontology revisions

Mila and Barbara continue to work on GO annotation of the blood-brain barrier (BBB) proteins, reviewed by Sweeney et al., 2019, and listed on our webpage. To date, Mila has curated 24 endothelial junction proteins, resulting in over 300 annotations, and 10 BBB ‘receptor-mediated transport’ proteins, resulting in over 150 annotations. Barbara has contributed over 250 annotations for 22 additional BBB transport proteins. In total, all ARUK-UCL projects have so far resulted in 8961 annotations for 1410 gene products (data from QuickGO, accessed 25th Nov 2019). Additionally, Mila’s work on endothelial junctions led her to identify and investigate out-of-date information about ‘cell-cell adherens’-related GO terms. As a result, Barbara has also been revising the cell junction ontology (e.g. GH issues 181191812018129) and coordinating related annotation reviews (e.g. GH issues 269026912700-2703) to ensure the information in GO is accurate and up to date. We thank Helen Attrill from FlyBase for her help with these revisions.

New microRNA annotation projects

Shirin Saverimuttu, our last year’s MSc project student who achieved a distinction and joint top marks in the Genetics of Human Disease MSc course, has joined our group and is annotating microRNAs (miRs) that regulate the expression of interleukins. This 4-month project, funded from the Functional Gene Annotation group’s 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 webpage.

Marios Makris, an intercalated BSc (iBSc) medical student, is going to continue GO annotation of miRs that regulate angiogenesis, an area previously curated by Vanessa Acquaah. 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 (http://greekc.org), the revision of the ‘DNA-binding transcription factor’ ontology is also leading to a revision of the list of proteins associated with the GO term GO:0003700 DNA-binding transcription factor activity (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: Barbara gave a presentation about GO and functional analysis tools at the Qatar University Laboratory Animal Research Center (LARC), Doha; Ruth gave a presentation and presented a poster about GO annotation of miRs at the RNA Informatics 2019 Conference at the Wellcome Genome Campus, Hinxton; Shirin presented a poster about GO curation of miRs in Alzheimer’s disease at the CompBioMed Conference 2019 in London. 

October: Ruth participated in discussions on ontology and annotation revisions at the GO Consortium Meeting in Berkeley, California, and gave a presentation at the GO Users Meeting entitled: Interpreting microRNA networks with GOShirin presented a poster about GO annotation of cardiovascular processes at the 8th Annual UCL Cardiovascular Symposium in London. 

November: Ruth participated in discussions about annotation of transcription factors at the eCOST meeting Gene Regulation Ensemble Effort for the Knowledge Commons in Sarajevo and gave a presentation about GO curation of miRs and participated in discussions on RNAcentral data integration and usability at the RNAcentral Consortium Meeting at the Wellcome Genome Campus, Hinxton.

Recent Publications

Panni S, Lovering RC, Porras P, Orchard S. Non-coding RNA regulatory networks. Biochim Biophys Acta Gene Regul Mech. 2019 Sep 4:194417. PMID:31493559.

Kramarz B and Lovering RC. Gene Ontology: A Resource for Analysis and Interpretation of Alzheimer’s Disease Data. In Wisniewski, T (ed), Alzheimer’s Disease (Chapter 2, pp. 23-36). November 21, 2019. Codon Publications. DOI: dx.doi.org/10.15586/alzheimersdisease.2019.ch2