Division of Infection and Pathway Medicine

Pathway Informatics Group

Headed by Professor Peter Ghazal, this group is working to develop a software infrastructure and novel applications which support our laboratory research in Pathway Biology.

Innate and adaptive immunity is created by a range of cellular processes carried out by a diversity of cells. In order to understand immunity, we must isolate these processes and identify how they arise from the complex system of genes, proteins, microRNAs, metabolites and more present inside each cell.

The chain of interactions between genes, proteins, microRNAs, metabolites, etc. is known as a pathway and in the Pathway Informatics Group we study the structure and function of these pathways, using computational and experimental approaches.

We have studied a range of systems including cholesterol metabolism, microRNA regulation, TNF regulation and interferon signalling at transcriptional, proteomic and flux levels. In particular, we have • comprehensively mapped out and modelled the structure and composition of a number of critical immune pathways to new levels of detail. • developed software tools to analyse the whole cell responses to infection • developed databases making available large transcriptional profiling datasets available • built software libraries to facilitate the use of high performance computing tools in statistical analysis.

Research Focus

We are primarily concerned with pathway analysis and transcriptional profiling.

Group members

Pathway Informatics is part of the Ghazal Research Group

Software & Databases

The GPX Macrophage Atlas (GPX-MEA) is a web resource for expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators.

Pathway Maps

For details of SBGN see 'Nicholas Le Novere, Michael Hucka, et al. The Systems Biology Graphical Notation. Nature Biotechology 27:735-741'.

Models

Our model of the cholesterol pathway, published in Biochimie 2012: S Watterson, ML Guerriero, et al. A model of flux regulation in the cholesterol biosynthesis pathway: Immune mediated graduated flux reduction versus statin-like led stepped flux reduction, Biochimie, http://dx.doi.org/10.1016/j.biochi.2012.05.024 (see Link below).

GPX Macrophage Atlas

The GPX Macrophage Atlas (GPX-MEA) is a web resource for expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators.

GPX

In addition to the macrophage-specific data-set, GPX also contains published datasets from a diverse range of transcription profiling studies.

PDQ Wizard

A 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.

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