Editor - Nancy Campbell
Protein-Protein Interaction (PPI) Curation
Since our last newsletter three months ago, Nancy has added a total of 357 binary interactions to the IntAct database by curating three publications. Firstly, 221 molecular interactions were added to the interactome of (serine/threonine) protein phosphatase 1 catalytic subunit alpha (PP1C) in atrial fibrillation patients. Secondly, 67 PPIs were added to the T-box 5 (Tbx5) interactome, which has a role in cardiac septation. Finally, 69 interactions were added to the solute carrier family 8 member A1 (Slc8a1) (also known as Ncx1) interactome, which is involved in cardiac conduction. Consequently, all of these interactomes are now freely available for download, visualisation & analysis via the PSICQUIC web server using appropriate software such as Cytoscape. The total number of PPIs curated to IMEx standard since this project started over four years ago is 3,630.
Nancy is now working with IntAct on their ‘Dark Space’ project (DSP). The DSP is an initiative led by the IntAct database to capture molecular interaction information that is reported in the literature but is not represented in IMEx databases. We are contributing to this project by prioritising the curation of a list of human genes known to be related to cardiac risk, and which we extracted from the publication entitled ‘Discovery and refinement of loci associated with lipid levels’, (PMID 24097068). Our priority list contains 20 genes that do not have any interaction data in IMEx databases or in the EBI-GOA-nonIntAct dataset.
Gene Ontology (GO) Curation
Our temporary curator, Vanessa, left us in December. Her mini-project was to curate miRNAs involved in regulating angiogenesis and to achieve this she read an impressive 140 papers, curated over 60 human miRNAs (as well as proteins) and generated over 1000 annotations, most of which are now publicly available from QuickGO. Many thanks to Vanessa for all the work she put in on this project. Due to efforts led by Rachael, the miRNA project has, to date, associated over 4,000 annotations to over 500 miRNAs.
We welcome Hao Chen who will be doing his MSc project with us. He will focus on curating miRNAs involved in familial hypercholesterolaemia.
Rachael attended the RNAcentral Consortium meeting on 6-7 November, 2017 where she contributed to a website feedback session and had useful discussions with representatives from various noncoding RNA databases.
In December 2017, Ruth attended the curation workshop on molecular and causal interactions which was held in Rome. A key goal of the workshop was to discuss how to capture directional relations between the interacting molecular components. Standardising the data captured by different groups will ensure these causal interaction annotation datasets can be included in system biology models of signalling pathways, enzyme reactions and transcriptional regulation.
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