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

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

Transcriptomic analysis of milk somatic cells in mastitis resistant and susceptible sheep upon challenge with Staphylococcus epidermidis and Staphylococcus aureus

<p>Abstract</p> <p>Background</p> <p>The existence of a genetic basis for host responses to bacterial intramammary infections has been widely documented, but the underlying mechanisms and the genes are still largely unknown. Previously, two divergent lines of sheep selected for high/low milk somatic cell scores have been shown to be respectively susceptible and resistant to intramammary infections by <it>Staphylococcus spp</it>. Transcriptional profiling with an 15K ovine-specific microarray of the milk somatic cells of susceptible and resistant sheep infected successively by <it>S. epidermidis </it>and <it>S. aureus </it>was performed in order to enhance our understanding of the molecular and cellular events associated with mastitis resistance.</p> <p>Results</p> <p>The bacteriological titre was lower in the resistant than in the susceptible animals in the 48 hours following inoculation, although milk somatic cell concentration was similar. Gene expression was analysed in milk somatic cells, mainly represented by neutrophils, collected 12 hours post-challenge. A high number of differentially expressed genes between the two challenges indicated that more T cells are recruited upon inoculation by <it>S. aureus </it>than <it>S. epidermidis</it>. A total of 52 genes were significantly differentially expressed between the resistant and susceptible animals. Further Gene Ontology analysis indicated that differentially expressed genes were associated with immune and inflammatory responses, leukocyte adhesion, cell migration, and signal transduction. Close biological relationships could be established between most genes using gene network analysis. Furthermore, gene expression suggests that the cell turn-over, as a consequence of apoptosis/granulopoiesis, may be enhanced in the resistant line when compared to the susceptible line.</p> <p>Conclusions</p> <p>Gene profiling in resistant and susceptible lines has provided good candidates for mapping the biological pathways and genes underlying genetically determined resistance and susceptibility towards <it>Staphylococcus </it>infections, and opens new fields for further investigation.</p

Modelling the kinetics of milk emission during machine milking in dairy ewes

The individual milking time is one of the aspects which affect the routine of milking in dairy ewes and the time to devote to this laborious task. The positive effect of an appropriate udder conformation in the reduction of manual interventions (stripping) during milking, have been clarified by numerous studies (Marie-Etancelin et al., 2001), leading to the development of appraisal methods of the udder which are being implemented in several breeding programs to improve udder morphology for milkability. On the other hand, a lack of knowledge on kinetics of the milk emission during machine milking still persists, mainly as a consequence of the difficulty of a large scale recording. Recently an automatic device able to follow individual kinetics of milk emission, developed by INRA (Ricard et al., 1995), was installed at the IZCS..

Heterogeneity of variance for type traits in the Montbeliarde cattle breed

This paper presents and discusses the estimation of genetic and residual (co-) variance components for conformation traits recorded in different environments using mixed linear models. Testing procedures for genetic parameters (genetic correlations between environments constant or equal to one, genetic correlation equal to one and constant intra-class correlations, homogeneity of variance-covariance components) are presented. These hypotheses were described via heteroskedastic univariate sire models taking into account genotype x environment interaction. An expectation-maximization (EM) algorithm was proposed for calculating restricted maximum likelihood (REML) estimates of the residual and genetic components of variances and co-variances. Likelihood ratio tests were suggested to assess hypotheses concerning genetic parameters. The procedures presented in the paper were used to analyze and to detect sources of variation on conformation traits in the Montbeliarde cattle breed using 24 301 progeny records of 528 sires. On all variables analyzed, several sources (stage of lactation, classifiers, type of housing) of heterogeneity of residual and genetic variances were clearly highlighted, but intra-class correlations between environments of type traits remained generally constant.Cet article présente et discute l’estimation des composantes de (co)variance (génétiques et résiduelles) de caractères de conformation mesurés entre milieux en situation d’hétéroscédasticité. Des tests d’homogénéité de certains paramètres (corrélations génétiques entre milieux constantes ou égales à 1, corrélations génétiques égales à 1 et corrélations intra-classes constantes, homogénéité des variances-covariances génétiques et résiduelles) intéressant les généticiens sont également présentés. Ces hypothèses sont décrites par un modèle père, unidimensionnel hétéroscédastique prenant en compte les interactions génotype x milieu. Un algorithme itératif d’espérance-maximisation (EM) est proposé pour calculer les estimées du maximum de vraisemblance restreinte (REML) des composantes résiduelles et génétiques de variance-covariance. Un test de rapport des vraisemblances restreintes est présenté pour tester les différentes hypothèses considérées. Les procédures développées sont utilisées pour l’analyse des notes de pointage de quelques caractères de morphologie de 24 301 performances d’animaux de race Montbéliarde issus de 528 pères. Sur l’ensemble des variables analysées, différentes sources (stade de lactation, pointeurs, type de logement) d’hétérogénéité des variances génétiques et résiduelles ont été mises en évidence mais en général L’héritabilité du caractère reste constante d’un milieu à l’autre