UCL Institute of Cardiovascular Science


Functional Gene Annotation - March 2020 Newsletter

3 March 2020

Editor - Barbara Kramarz

image of typewriter inserted to represent newsletter

Many thanks and farewell to Dr Milagros Rodríguez-López

Dr Milagros Rodríguez-López, EMBL-EBI, was working on the ARUK-UCL neuroinflammation project from February till December 2019. Throughout this collaboration Mila worked closely with Barbara on GO annotation of, firstly, microglial proteins implicated in Alzheimer’s disease, and then on the endothelial junction and transport proteins important for the blood-brain barrier processes. Mila’s curation work also led to ontology revisions and updates of ‘cell-cell adherens’-related GO terms. We thank Mila for her contributions to this project and we wish her every success in the future.

Blood-brain barrier annotation progress

Mila completed the GO annotation of the 24 ‘endothelial connection’ proteins and 10 ‘receptor-mediated transport’ proteins, listed on our webpage, resulting in 317 and 177 GO annotations, respectively. In addition, Mila curated 8 out of 47 ‘solute carrier-mediated transport’ proteins contributing 72 annotations, whereas Barbara has contributed annotations for 10 more proteins from this same list resulting in 78 annotations. Barbara has also completed the annotation of ‘ion transport’ proteins, resulting in 362 annotations for 16 proteins. Barbara is continuing the curation of the remaining ‘solute carrier-mediated transport’ proteins (data from QuickGO, accessed 1st March 2020). 

Annotation of microRNAs regulating interleukins

Shirin has been annotating microRNAs that regulate the expression of interleukins since October 2019. Throughout this project Shirin has curated a total of 59 papers, identified in miRTarBase and through PubMed searches, and contributed over 450 annotations for more than 44 microRNAs.

New microRNA annotation projects

We are pleased to welcome two MSc students, Katherine Thurlow and Sandra De Miranda Pinheiro. Katherine will be using GO to capture knowledge about microRNAs with roles in the blood-brain barrier, whereas Sandra will be annotating microRNAs that regulate the APP and BACE1 Alzheimer’s disease genes.

ARUK-UCL Annotation Statistics

In total, all ARUK-UCL projects, including the GO annotation of proteins interacting with amyloid-beta and tau, microglial proteins and blood-brain barrier proteins, as well as microRNAs regulating the expression of proteins implicated in Alzheimer’s disease, have so far resulted in 10,252 annotations for 1,651 distinct gene products, including: 8,192 annotations for 1,332 proteins; 1,673 annotations for 297 non-coding RNAs (mainly microRNAs); and 387 annotations for 22 protein-containing complexes (data from QuickGO, accessed 1st March 2020). 

Meetings attended

Shirin was awarded a Short Term Scientific Mission (STSM) grant from the European Cooperation In Science and Technology (COST) organisation, which allowed her to travel to Università della Calabria in southern Italy for a week-long knowledge exchange meeting with Dr Simona Panni. During this time Simona trained Shirin in capturing molecular interactions between microRNAs and their mRNA targets using the IntAct curation tool, whereas Shirin shared with Simona her knowledge about GO annotation of microRNAs, and trained Simona in using the Gene Ontology Annotation (GOA) curation tool.

Ruth organised a small meeting at UCL in January, funded by the GREEKC COST project, which focused on developing guidelines for the curation of DNA binding transcription factors (dbTFs) and reviewing the GO annotation of 400 possible human dbTFs. In February, Ruth presented the progress of this project at the Università della Calabria, Rende, Italy. At this meeting several researchers agreed to help to complete this task, which would lead to a 2020 list of all known human dbTfs being associated with the GO term GO:0003700 DNA-binding transcription factor activity. 

Introduction to Bioinformatics and GO workshop

24th - 25th June 2020

If you would like to attend our popular free two-day workshops, please use the Eventbrite site to register. This workshop is funded by ARUK and provides an overview of several biological knowledgebases, as well as an introduction to GO and functional analysis tools.