A classification of tasks for the systematic study of immune response using functional genomics data

• Published in: Parasitology Vol. 132; no. 2; pp. 157 - 167
• Main Authors: HEDELER, C., PATON, N. W., BEHNKE, J. M., BRADLEY, J. E., HAMSHERE, M. G., ELSE, K. J.
• Format: Journal Article
• Language: English
• Published: Cambridge, UK Cambridge University Press 01.02.2006
• Subjects: Allergy and Immunology - classification; Animals; Biological and medical sciences; classification; Data Collection - classification; Data Collection - methods; Data Collection - standards; Experiments; Fundamental and applied biological sciences. Psychology; Gene expression; General aspects; General aspects and techniques. Study of several systematic groups. Models; Genomics - methods; Heligmosomoides polygyrus; Hypotheses; Immune system; Immunity, Active - genetics; Immunization; intestinal nematode; Invertebrates; Mice; Nemathelminthia. Plathelmintha; Nematospiroides dubius - immunology; Oligonucleotide Array Sequence Analysis - methods; Pathogens; Statistics as Topic - classification; Statistics as Topic - methods; Statistics as Topic - standards; Strongylida Infections - genetics; Strongylida Infections - immunology; Studies; systematic immunological bioinformatics; Task Performance and Analysis; Trichuriasis - genetics; Trichuriasis - immunology; Trichuris - immunology; Trichuris muris; classification; systematic immunological bioinformatics; intestinal nematode; Immune response; Functional response; Taxonomy; Classification; Helmintha; Parasite; Nemathelminthia; Invertebrata; Nematoda; Defense
• ISSN: 0031-1820; 1469-8161
• DOI: 10.1017/S0031182005008796

A full understanding of the immune system and its responses to infection by different pathogens is important for the development of anti-parasitic vaccines. A growing number of large-scale experimental techniques, such as microarrays, are being used to gain a better understanding of the immune system. To analyse the data generated by these experiments, methods such as clustering are widely used. However, individual applications of these methods tend to analyse the experimental data without taking publicly available biological and immunological knowledge into account systematically and in an unbiased manner. To make best use of the experimental investment, to benefit from existing evidence, and to support the findings in the experimental data, available biological information should be included in the analysis in a systematic manner. In this review we present a classification of tasks that shows how experimental data produced by studies of the immune system can be placed in a broader biological context. Taking into account available evidence, the classification can be used to identify different ways of analysing the experimental data systematically. We have used the classification to identify alternative ways of analysing microarray data, and illustrate its application using studies of immune responses in mice to infection with the intestinal nematode parasites Trichuris muris and Heligmosomoides polygyrus.