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December 2018

Editor – Barbara Kramarz

Congratulations to Rachael on her new position at SciBite!

Rachael will be leaving us at the end of December to take up a new position as a biocurator at SciBite on the Wellcome Trust Genome Campus in Cambridge. SciBite develops technology using ontologies to enable simpler extraction and analysis of data from life science texts. Rachael, a highly cited researcher in Web of Science, has been a great asset to our team and she will continue to act as an advisor for the microRNA project. Rachael, we will miss you!

Annotation of microglial proteins and regulatory microRNAs

Barbara and Rachael have been involved in annotation of microglial proteins and microRNAs, which regulate their expression. Twenty one of the 40 prioritised proteins have been annotated so far and the regulatory microRNAs have been identified and annotated for 31 of the prioritised proteins. A preliminary network analysis has revealed that four of these microRNAs also target APP (Figure 1).

 

Figure 1. A fragment of a Cytoscape network showing APP gene products being targeted by four different regulatory microRNAs.

 

Figure 1. A fragment of a Cytoscape network showing APP gene products being targeted by four different regulatory microRNAs. Colours within the APP node represent GO terms, describing inflammation and immune system processes, which have been associated with APP gene products in GO annotations. Figure provided by Dr Rachael Huntley.

 

 

ARUK-UCL Gene Ontology annotation progress

Collectively, all of the ARUK-funded work, has thus far resulted in 5634 GO annotations to 864 gene products, including proteins, microRNAs and macromolecular protein complexes involved in interactions with amyloid-beta and tau as well as in dementia-relevant microglial processes. Of these, 3969 GO annotations have been associated with 495 human gene products (EBI statistics, QuickGO accessed: 27th November 2018).

Meetings attended

7th September 2018, Barbara gave a 3-minute flash presentation at the ARUK UCL Network Scientific Meeting, introducing the GO resource to the ARUK UCL Network community, and presented a poster, which outlined our work and its applications in detail.

17th-19th October 2018, GO Consortium Meeting, the 20th GO Anniversary, Montreal, Canada: Ruth participated in discussions about capturing biological knowledge about transcription.

19th October 2018, RNAcentral Consortium Meeting, EMBL-EBI, Hinxton, UK: Rachael participated in discussions on noncoding RNA data integration and usability.

15th November 2018, ARUK-UCL Gene Ontology (GO) Project Scientific Advisory Panel Meeting: Ruth, Barbara and Rachael provided a summary of annotation progress and challenges. Professors Paul Whiting(1) and John Hardy(2) from UCL and Professors Nigel Hooper(3) and David Brough(4) from the University of Manchester shared their expertise and offered advice regarding future project goals and neuroinflammation annotation priorities. Sandra Orchard(5) (EMBL-EBI) provided an overview of UniProt’s Alzheimer’s-focused biocuration efforts. The next Scientific Advisory Panel meeting will be held in London in spring 2019.

Recent Publications

Kramarz B, Roncaglia P, Meldal BHM, Huntley RP, Martin MJ, Orchard S, Parkinson H, Brough D, Bandopadhyay R, Hooper NM, Lovering RC. Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer’s Disease Data. Genes. 2018 Nov 29.

Köhler S, Carmody L, Vasilevsky N, … Lovering RC, … Haendel MA, Mungall C, Robinson PN. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 2018 Nov 22. PMID:30476213.

The Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. 2018 Nov 5. PMID:30395331.

The RNAcentral Consortium. RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res. 2018 Nov 5. PMID:30395267.