Editor – Ruth Lovering
Many thanks and farewell to Dr Barbara Kramarz
After 4 years as a member of the group, Barbara is now starting a new role as a Lecturer and Programme Coordinator at Oryx Universal College in Doha, Qatar, in partnership with Liverpool John Moores University. In this new role Barbara will build on her higher education teaching experience, gained at UCL, and as a Fellow of the Higher Education Academy. I would like to thank Barbara for all the work she has done at UCL. She was responsible not only for protein and microRNA curation, as part of several different projects, but also contributed to the creation or revision of over 300 GO terms. In addition, her work as Project Coordinator of several ARUK GO annotation projects was key to its success and her teaching skills were much appreciated by the MSc student projects. We wish her all the best and good luck in her lectureship.
Blood-brain barrier annotation progress
The annotation project focused on transport at blood-brain barrier is drawing to a close, with Shirin now curating of this domain. Following the review of over 170 articles and the creation of more than 1,400 GO annotations, only 5 of the 81 human proteins prioritised for annotation by this project still need to be curated. For example SLC29A4, is now associated with GO terms describing the uptake of: serotonin, norepinephrine, histamine, dopamine, epinephrine as well as its role as a neurotransmitter transmembrane transporter in the transport across the blood brain barrier. None of this information was previously associated with SLC29A4, thus, ARUK funding is enabling more comprehensive annotation of Alzheimer’s relevant proteins.
ARUK-UCL Annotation Statistics
In total, all ARUK-UCL projects have resulted in 11,766 annotations for 1,854 distinct gene products, of which 8,554 annotations are associated with 1,131 human gene products (data from QuickGO, 1st June 2020).
Other annotation projects
Following the lockdown in the UK, we are pleased to welcome two more MSc students, Heather Gunn and Renzhi Su. Heather will be using GO to describe the subunits of PI3Kinase, and her project will be co-supervised by Paul Frankel, who brings signalling expertise to the project. Whereas Renzhi will be annotating microRNAs that regulate the PPARG and their potential role in hypertension, his project will be co-supervised by Lucie Clapp, Lucie was key to setting up the UCL-wide pulmonary arterial hypertension consortium.
Despite the lockdown, Ruth has continued to collaborate with GREEKC and has been working closely with Pascale Gaudet and Colin Logie, and many others in the GO Consortium to create a comprehensive list of DNA binding transcription factors and to ensure that the GO Consortium database represents these appropriately. Together this collaboration has led to the checking of over 2000 annotations and revision of over 400, with around 500 annotations still to check.
Ruth and Pascale organised a ‘remove’ 3-day workshop at the end of April, attended by 14 people (mostly GO curators) to promote the revised ontology, and associated guidelines, for the annotation of DNA binding transcription factors, transcription coregulators and general transcription factors.
In May Ruth and Shirin attended the remote 3-day GO Consortium meeting, due to be held in Paris, where progess to moving GO annotation from simple linear annotations to annotation models was presented, along with progress on increasing the import of Reactome data.
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- Hall CL, Gurha P, Sabater-Molina M, Asimaki A, Futema M, Lovering RC, Suárez MP, Aguilera B, Molina P, Zorio E, Coarfa C, Robertson MJ, Cheedipudi SM, Ng KE, Delaney P, Hernández JP, Pastor F, Gimeno JR, McKenna WJ, Marian AJ, Syrris P. RNA sequencing-based transcriptome profiling of cardiac tissue implicates novel putative disease mechanisms in FLNC-associated arrhythmogenic cardiomyopathy. Int J Cardiol. 2020. 302:124-130. PMID: 31843279.
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