Research Focus
We are primarily concerned with pathway analysis and transcriptional profiling.
Pathway Analysis
Edinburgh Pathway Notation (EPN)
The Edinburgh Pathway Notation (EPN) has been developed in collaboration with researchers in the Edinburgh School of Informatics to enable the graphical representation of pathways curated during our Pathway Biology research.
EPN uses a logical state-transition representation to describe biological pathways, fulfils the objective of providing a graphical notation that is useable by biologists and serves as the basis for computational model development.
Systems Biology Graphical Notation project (SBGN)
We are a member of the international Systems Biology Graphical Notation project (SBGN) which aims to bring consistency and uniformity to the graphical expression of network diagrams in biology.
Infobiomed
Our work in Infobiomed is to harness and integrate pathogen and host-specific pathway, genotype, 'omic' and clinical data with novel bioinformatics prediction techniques.
This work is aimed at establishing methods and approaches for the future identification of novel biomarkers and the development of enhanced diagnoses and treatments for infectious disease using a pathway biology approach.
This project is a collaboration of over 20 European research groups which aims to combine Medical- and Bio- Informatics expertise and to facilitate the discovery of novel diagnostic and therapeutic methods.
Databases
MIARE: Minimum Information About an RNAi Experiment is a set of reporting guidelines that describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results. MIARE forms part of a larger effort to develop RNAi data standards that include a data model, data exchange format, controlled vocabulary and supporting software tools.
PDQ Wizard: This web-based tool that enables the rapid classification and prioritisation of large lists of gene and protein identifiers (GenBank, RefSeq, UniGene, Entrez Gene, Gene Symbols, SwissProt) using the PubMed biomedical literature database.
Biolayout: This is an open-source data visualisation tool co-developed by Dr Tom Freeman. This tool is finding increasing use in the rapid analysis of large transcription datasets within the Division of Pathway Medicine.
Transcriptional Profiling
Researchers at the Division of Pathway Medicine have over a decade of experience in the design, development and application of microarray technology.
Since our inception we have advised on the experimental design and analysis of over 300 microarray studies, and developed a number of databases, automated data handling applications and analysis tools.
Edinburgh National Translational Cancer Research Network Centre (NTRAC)
As a partner in the Edinburgh National Translational Cancer Research Network Centre (NTRAC) we have added additional functionality to our GPX database, enabling the storage of genotyping expression data and initiating work towards integration of the resource with clinical databases.
Databases
GPX: This is a transcriptional profiling database containing data from a diverse range of transcription profiling studies carried out at GTI and elsewhere. Public access to published datasets is available via GPX Discovery.
GPX Macrophage Atlas (GPX-MEA): This is a focused web resource for expression-based studies of a range of macrophage cell types following treatment with pathogens and immune modulators.
Other tools
Other tools developed within the Division to support transcriptional analyses include FastSnap (data handling tool), ThX (automated microarray analysis), IDD-Genes (GRID computing demonstrator) and a custom array LIMS system.
This article was published on Apr 12, 2012