Open Access

Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (Open Access publication)

  • Florence Jaffrézic1Email author,
  • Dirk-Jan de Koning2,
  • Paul J Boettcher3,
  • Agnès Bonnet4,
  • Bart Buitenhuis5,
  • Rodrigue Closset6,
  • Sébastien Déjean7,
  • Céline Delmas8,
  • Johanne C Detilleux9,
  • Peter Dovč10,
  • Mylène Duval8,
  • Jean-Louis Foulley1,
  • Jakob Hedegaard5,
  • Henrik Hornshøj5,
  • Ina Hulsegge11,
  • Luc Janss5,
  • Kirsty Jensen2,
  • Li Jiang5,
  • Miha Lavrič10,
  • Kim-Anh Lê Cao7, 8,
  • Mogens Sandø Lund5,
  • Roberto Malinverni3,
  • Guillemette Marot1,
  • Haisheng Nie12,
  • Wolfram Petzl13,
  • Marco H Pool11,
  • Christèle Robert-Granié8,
  • Magali San Cristobal4,
  • Evert M van Schothorst14,
  • Hans-Joachim Schuberth15,
  • Peter Sørensen5,
  • Alessandra Stella3,
  • Gwenola Tosser-Klopp4,
  • David Waddington2,
  • Michael Watson16,
  • Wei Yang17,
  • Holm Zerbe13 and
  • Hans-Martin Seyfert17
Genetics Selection Evolution200739:633

DOI: 10.1186/1297-9686-39-6-633

Received: 10 May 2007

Accepted: 6 July 2007

Published: 6 December 2007

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.

Keywords

quality control differentially expressed genes mastitis resistance microarray data normalisation

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Authors’ Affiliations

(1)
INRA, UR337, (INRA_J)
(2)
Roslin Institute, (ROSLIN)
(3)
Parco Tecnologico Padano (PTP)
(4)
INRA, UMR444, (INRA_T)
(5)
University of Aarhus, (AARHUS)
(6)
University of Liège, (ULg2)
(7)
Université Paul Sabatier, (INRA_T)
(8)
INRA, UR631, (INRA_T)
(9)
Faculty of Veterinary Medicine, University of Liège, (ULg1)
(10)
University of Ljubljana, (SLN)
(11)
Animal Sciences Group Wageningen UR
(12)
Wageningen University and Research Centre, (WUR)
(13)
Ludwig-Maximilians-University
(14)
RIKILT-Institute of Food Safety, (WUR)
(15)
University of Veterinary Medicine
(16)
Institute for Animal Health, (IAH)
(17)
Research Institute for the Biology of Farm Animals

Copyright

© INRA, EDP Sciences 2007

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