Date(s) - 05/02/2020
9:00 am - 5:00 pm

NIHR Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London
16th Floor, Tower Wing, Guy’s Hospital, Great Maze Pond

Course description

The contextualisation of molecular signatures such as sets of differentially expressed genes from transcriptomics experiments, requires mapping to known biological pathways and networks. This course gives an introduction to commonly used pathway resources, and describes approaches to identify enriched pathways from gene expression data. The utility of molecular interaction networks for data interpretation is also explained and the visual exploration of biological networks with the popular program Cytoscape is described.

Learning objectives

By the end of the session, participants should be able to:

  • Understand the utility of representing biological information as a network
  • Be able to explore information in commonly used pathway resources such as Reactome
  • Understand the basis of approaches to identify enriched pathways, and Gene Ontology terms
  • Be able to use the popular program Cytoscape to visually explore molecular interaction networks and molecular pathways
  • Use Cytoscape for exploration of gene expression data

At the end of the workshop students will have a broad overview of methods for contextualising sets of differentially expressed genes in the context of molecular pathways and protein interaction networks.

About the trainer

Dr Mansoor Saqi is Head of Translational Bioinformatics at the Biomedical Research Centre at Guys and St Thomas’s and Kings College London. His research interests include data integration, analysis of integrated biological networks and disease stratification. He has held positions at the Data Sciences Institute, Imperial College London, and at the CNRS (EISBM, Lyon). Previous to that he was a Principal Investigator in Bioinformatics at the Centre for Computational and Systems Biology at Rothamsted Research, UK, and before that he was a Senior Lecturer in Bioinformatics at Barts and The London School of Medicine.

Dr Konstantina Dimitrakopoulou is Senior Bioinformatician at the Translational Bioinformatics Platform of the Biomedical Research Centre at Guy’s and St Thomas’s. Her research interests include data integration and network medicine. She holds an M.S. and a PhD, from the Interuniversity Postgraduate Programme on Biomedical Engineering (University of Patras, Greece). She continued her work in the Centre for Cancer Biomarkers (CCBIO) and Computational Biology Unit (CBU), at Dept. Informatics at University of Bergen (Norway) and later in the Institute of Marine Research (Norway).