Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (Open Access publication)
Year: 2007
Type: article
Abstract: A large variety of methods has been proposed in the literature for microarray data analysis. The aim of this paper was to present techniques used by the EADGENE (European Animal Disease Genomics Network of Excellence) WP1.4 participants for data quality control, normalisation and statistical methods for the detection of differentially expressed genes in order to provide some more general data analysis guidelines. All the workshop participants were given a real data set obtained in an EADGENE funded microarray study looking at the gene expression changes following artificial infection with two different mastitis causing bacteria: Escherichia coli and Staphylococcus aureus. It was reassuring to see that most of the teams found the same main biological results. In fact, most of the differentially expressed genes were found for infection by E. coli between uninfected and 24 h challenged udder quarters. Very little transcriptional variation was observed for the bacteria S. aureus. Lists of differentially expressed genes found by the different research teams were, however, quite dependent on the method used, especially concerning the data quality control step. These analyses also emphasised a biological problem of cross-talk between infected and uninfected quarters which will have to be dealt with for further microarray studies.
Source: Genetics Selection Evolution
Authors: Florence Jaffrézic, Dirk-Jan de Koning, Paul J Boettcher, Agnès Bonnet, Bart Buitenhuis, Rodrigue Closset, Sébastien Déjean, Céline Delmas, Johanne C Detilleux, Peter Dovč, Mylène Duval, Jean-Louis Foulley, Jakob Hedegaard, Henrik Hornshøj, Ina Hulsegge, Luc Janss, Kirsty Jensen, Li Jiang, Miha Lavrič, Kim-Anh Lê Cao, Mogens Sandø Lund, Roberto Malinverni, Guillemette Marot, Haisheng Nie, Wolfram Petzl, Marco H Pool, Christèle Robert-Granié, Magali San Cristobal, Evert M van Schothorst, Hans-Joachim Schuberth, Peter Sørensen, Alessandra Stella, Gwenola Tosser-Klopp, David Waddington, Michael Watson, Wei Yang, Holm Zerbe, Hans-Martin Seyfert
Institutions: Institut National de la Recherche Agronomique, Roslin Institute, Parco Tecnologico Padano, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Aarhus University, University of Liège, Université Toulouse III - Paul Sabatier, University of Ljubljana, Wageningen University & Research, Ludwig-Maximilians-Universität München, University of Veterinary Medicine Hannover, Foundation, The Pirbright Institute, Research Institute for Farm Animal Biology (FBN)
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
SDG: Zero hunger
Open Access status: hybrid
Estimated APC paid: $2,390
OpenAlex ID: W2145834815