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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Analysis of the real EADGENE data set: Multivariate approaches and post analysis (<italic>Open Access publication</italic>)</title><author><name sortKey="S Rensen, Peter" sort="S Rensen, Peter" uniqKey="S Rensen P" first="Peter" last="S Rensen">Peter S Rensen</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Bonnet, Agnes" sort="Bonnet, Agnes" uniqKey="Bonnet A" first="Agnès" last="Bonnet">Agnès Bonnet</name><affiliation><nlm:aff id="I2">INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Buitenhuis, Bart" sort="Buitenhuis, Bart" uniqKey="Buitenhuis B" first="Bart" last="Buitenhuis">Bart Buitenhuis</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Closset, Rodrigue" sort="Closset, Rodrigue" uniqKey="Closset R" first="Rodrigue" last="Closset">Rodrigue Closset</name><affiliation><nlm:aff id="I3">Faculty of Veterinary Medicine, University of Liege, Liege, Belgium</nlm:aff></affiliation></author><author><name sortKey="Dejean, Sebastien" sort="Dejean, Sebastien" uniqKey="Dejean S" first="Sébastien" last="Déjean">Sébastien Déjean</name><affiliation><nlm:aff id="I4">Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse, France</nlm:aff></affiliation></author><author><name sortKey="Delmas, Celine" sort="Delmas, Celine" uniqKey="Delmas C" first="Céline" last="Delmas">Céline Delmas</name><affiliation><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Duval, Mylene" sort="Duval, Mylene" uniqKey="Duval M" first="Mylène" last="Duval">Mylène Duval</name><affiliation><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Glass, Liz" sort="Glass, Liz" uniqKey="Glass L" first="Liz" last="Glass">Liz Glass</name><affiliation><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff></affiliation></author><author><name sortKey="Hedegaard, Jakob" sort="Hedegaard, Jakob" uniqKey="Hedegaard J" first="Jakob" last="Hedegaard">Jakob Hedegaard</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Hornsh J, Henrik" sort="Hornsh J, Henrik" uniqKey="Hornsh J H" first="Henrik" last="Hornsh J">Henrik Hornsh J</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Hulsegge, Ina" sort="Hulsegge, Ina" uniqKey="Hulsegge I" first="Ina" last="Hulsegge">Ina Hulsegge</name><affiliation><nlm:aff id="I7">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Jaffrezic, Florence" sort="Jaffrezic, Florence" uniqKey="Jaffrezic F" first="Florence" last="Jaffrézic">Florence Jaffrézic</name><affiliation><nlm:aff id="I8">INRA, UR337 Station de génétique quantitative et appliquée, Jouy-en-Josas, 78350, France</nlm:aff></affiliation></author><author><name sortKey="Jensen, Kirsty" sort="Jensen, Kirsty" uniqKey="Jensen K" first="Kirsty" last="Jensen">Kirsty Jensen</name><affiliation><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff></affiliation></author><author><name sortKey="Jiang, Li" sort="Jiang, Li" uniqKey="Jiang L" first="Li" last="Jiang">Li Jiang</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="De Koning, Dirk Jan" sort="De Koning, Dirk Jan" uniqKey="De Koning D" first="Dirk-Jan" last="De Koning">Dirk-Jan De Koning</name><affiliation><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff></affiliation></author><author><name sortKey="Cao, Kim Anh Le" sort="Cao, Kim Anh Le" uniqKey="Cao K" first="Kim-Anh Lê" last="Cao">Kim-Anh Lê Cao</name><affiliation><nlm:aff id="I4">Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse, France</nlm:aff></affiliation><affiliation><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Nie, Haisheng" sort="Nie, Haisheng" uniqKey="Nie H" first="Haisheng" last="Nie">Haisheng Nie</name><affiliation><nlm:aff id="I9">Animal Breeding and Genomics Centre, Wageningen University and Research Centre, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Petzl, Wolfram" sort="Petzl, Wolfram" uniqKey="Petzl W" first="Wolfram" last="Petzl">Wolfram Petzl</name><affiliation><nlm:aff id="I10">Clinic for Ruminants, Ludwig-Maximilians-University, Munich, Germany</nlm:aff></affiliation></author><author><name sortKey="Pool, Marco H" sort="Pool, Marco H" uniqKey="Pool M" first="Marco H" last="Pool">Marco H. Pool</name><affiliation><nlm:aff id="I7">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Robert Granie, Christele" sort="Robert Granie, Christele" uniqKey="Robert Granie C" first="Christèle" last="Robert-Granié">Christèle Robert-Granié</name><affiliation><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="San Cristobal, Magali" sort="San Cristobal, Magali" uniqKey="San Cristobal M" first="Magali" last="San Cristobal">Magali San Cristobal</name><affiliation><nlm:aff id="I2">INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Lund, Mogens Sand" sort="Lund, Mogens Sand" uniqKey="Lund M" first="Mogens Sand" last="Lund">Mogens Sand Lund</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Van Schothorst, Evert M" sort="Van Schothorst, Evert M" uniqKey="Van Schothorst E" first="Evert M" last="Van Schothorst">Evert M. Van Schothorst</name><affiliation><nlm:aff id="I11">Food Bioactives Group, RIKILT-Institute of Food Safety, Wageningen University and Research Centre, Wageningen, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Schuberth, Hans Joachim" sort="Schuberth, Hans Joachim" uniqKey="Schuberth H" first="Hans-Joachim" last="Schuberth">Hans-Joachim Schuberth</name><affiliation><nlm:aff id="I12">Immunology Unit, University of Veterinary Medicine, Hannover, Germany</nlm:aff></affiliation></author><author><name sortKey="Seyfert, Hans Martin" sort="Seyfert, Hans Martin" uniqKey="Seyfert H" first="Hans-Martin" last="Seyfert">Hans-Martin Seyfert</name><affiliation><nlm:aff id="I13">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff></affiliation></author><author><name sortKey="Tosser Klopp, Gwenola" sort="Tosser Klopp, Gwenola" uniqKey="Tosser Klopp G" first="Gwenola" last="Tosser-Klopp">Gwenola Tosser-Klopp</name><affiliation><nlm:aff id="I12">Immunology Unit, University of Veterinary Medicine, Hannover, Germany</nlm:aff></affiliation></author><author><name sortKey="Waddington, David" sort="Waddington, David" uniqKey="Waddington D" first="David" last="Waddington">David Waddington</name><affiliation><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff></affiliation></author><author><name sortKey="Watson, Michael" sort="Watson, Michael" uniqKey="Watson M" first="Michael" last="Watson">Michael Watson</name><affiliation><nlm:aff id="I14">Informatics Group, Institute for Animal Health, Compton, Newbury, Berks RG20 7NN, UK</nlm:aff></affiliation></author><author><name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name><affiliation><nlm:aff id="I13">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff></affiliation></author><author><name sortKey="Zerbe, Holm" sort="Zerbe, Holm" uniqKey="Zerbe H" first="Holm" last="Zerbe">Holm Zerbe</name><affiliation><nlm:aff id="I10">Clinic for Ruminants, Ludwig-Maximilians-University, Munich, Germany</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18053574</idno><idno type="pmc">2682812</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682812</idno><idno type="RBID">PMC:2682812</idno><idno type="doi">10.1186/1297-9686-39-6-651</idno><date when="2007">2007</date><idno type="wicri:Area/Pmc/Corpus">000236</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Analysis of the real EADGENE data set: Multivariate approaches and post analysis (<italic>Open Access publication</italic>)</title><author><name sortKey="S Rensen, Peter" sort="S Rensen, Peter" uniqKey="S Rensen P" first="Peter" last="S Rensen">Peter S Rensen</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Bonnet, Agnes" sort="Bonnet, Agnes" uniqKey="Bonnet A" first="Agnès" last="Bonnet">Agnès Bonnet</name><affiliation><nlm:aff id="I2">INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Buitenhuis, Bart" sort="Buitenhuis, Bart" uniqKey="Buitenhuis B" first="Bart" last="Buitenhuis">Bart Buitenhuis</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Closset, Rodrigue" sort="Closset, Rodrigue" uniqKey="Closset R" first="Rodrigue" last="Closset">Rodrigue Closset</name><affiliation><nlm:aff id="I3">Faculty of Veterinary Medicine, University of Liege, Liege, Belgium</nlm:aff></affiliation></author><author><name sortKey="Dejean, Sebastien" sort="Dejean, Sebastien" uniqKey="Dejean S" first="Sébastien" last="Déjean">Sébastien Déjean</name><affiliation><nlm:aff id="I4">Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse, France</nlm:aff></affiliation></author><author><name sortKey="Delmas, Celine" sort="Delmas, Celine" uniqKey="Delmas C" first="Céline" last="Delmas">Céline Delmas</name><affiliation><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Duval, Mylene" sort="Duval, Mylene" uniqKey="Duval M" first="Mylène" last="Duval">Mylène Duval</name><affiliation><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Glass, Liz" sort="Glass, Liz" uniqKey="Glass L" first="Liz" last="Glass">Liz Glass</name><affiliation><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff></affiliation></author><author><name sortKey="Hedegaard, Jakob" sort="Hedegaard, Jakob" uniqKey="Hedegaard J" first="Jakob" last="Hedegaard">Jakob Hedegaard</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Hornsh J, Henrik" sort="Hornsh J, Henrik" uniqKey="Hornsh J H" first="Henrik" last="Hornsh J">Henrik Hornsh J</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Hulsegge, Ina" sort="Hulsegge, Ina" uniqKey="Hulsegge I" first="Ina" last="Hulsegge">Ina Hulsegge</name><affiliation><nlm:aff id="I7">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Jaffrezic, Florence" sort="Jaffrezic, Florence" uniqKey="Jaffrezic F" first="Florence" last="Jaffrézic">Florence Jaffrézic</name><affiliation><nlm:aff id="I8">INRA, UR337 Station de génétique quantitative et appliquée, Jouy-en-Josas, 78350, France</nlm:aff></affiliation></author><author><name sortKey="Jensen, Kirsty" sort="Jensen, Kirsty" uniqKey="Jensen K" first="Kirsty" last="Jensen">Kirsty Jensen</name><affiliation><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff></affiliation></author><author><name sortKey="Jiang, Li" sort="Jiang, Li" uniqKey="Jiang L" first="Li" last="Jiang">Li Jiang</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="De Koning, Dirk Jan" sort="De Koning, Dirk Jan" uniqKey="De Koning D" first="Dirk-Jan" last="De Koning">Dirk-Jan De Koning</name><affiliation><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff></affiliation></author><author><name sortKey="Cao, Kim Anh Le" sort="Cao, Kim Anh Le" uniqKey="Cao K" first="Kim-Anh Lê" last="Cao">Kim-Anh Lê Cao</name><affiliation><nlm:aff id="I4">Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse, France</nlm:aff></affiliation><affiliation><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Nie, Haisheng" sort="Nie, Haisheng" uniqKey="Nie H" first="Haisheng" last="Nie">Haisheng Nie</name><affiliation><nlm:aff id="I9">Animal Breeding and Genomics Centre, Wageningen University and Research Centre, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Petzl, Wolfram" sort="Petzl, Wolfram" uniqKey="Petzl W" first="Wolfram" last="Petzl">Wolfram Petzl</name><affiliation><nlm:aff id="I10">Clinic for Ruminants, Ludwig-Maximilians-University, Munich, Germany</nlm:aff></affiliation></author><author><name sortKey="Pool, Marco H" sort="Pool, Marco H" uniqKey="Pool M" first="Marco H" last="Pool">Marco H. Pool</name><affiliation><nlm:aff id="I7">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Robert Granie, Christele" sort="Robert Granie, Christele" uniqKey="Robert Granie C" first="Christèle" last="Robert-Granié">Christèle Robert-Granié</name><affiliation><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="San Cristobal, Magali" sort="San Cristobal, Magali" uniqKey="San Cristobal M" first="Magali" last="San Cristobal">Magali San Cristobal</name><affiliation><nlm:aff id="I2">INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff></affiliation></author><author><name sortKey="Lund, Mogens Sand" sort="Lund, Mogens Sand" uniqKey="Lund M" first="Mogens Sand" last="Lund">Mogens Sand Lund</name><affiliation><nlm:aff id="I1">University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</nlm:aff></affiliation></author><author><name sortKey="Van Schothorst, Evert M" sort="Van Schothorst, Evert M" uniqKey="Van Schothorst E" first="Evert M" last="Van Schothorst">Evert M. Van Schothorst</name><affiliation><nlm:aff id="I11">Food Bioactives Group, RIKILT-Institute of Food Safety, Wageningen University and Research Centre, Wageningen, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Schuberth, Hans Joachim" sort="Schuberth, Hans Joachim" uniqKey="Schuberth H" first="Hans-Joachim" last="Schuberth">Hans-Joachim Schuberth</name><affiliation><nlm:aff id="I12">Immunology Unit, University of Veterinary Medicine, Hannover, Germany</nlm:aff></affiliation></author><author><name sortKey="Seyfert, Hans Martin" sort="Seyfert, Hans Martin" uniqKey="Seyfert H" first="Hans-Martin" last="Seyfert">Hans-Martin Seyfert</name><affiliation><nlm:aff id="I13">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff></affiliation></author><author><name sortKey="Tosser Klopp, Gwenola" sort="Tosser Klopp, Gwenola" uniqKey="Tosser Klopp G" first="Gwenola" last="Tosser-Klopp">Gwenola Tosser-Klopp</name><affiliation><nlm:aff id="I12">Immunology Unit, University of Veterinary Medicine, Hannover, Germany</nlm:aff></affiliation></author><author><name sortKey="Waddington, David" sort="Waddington, David" uniqKey="Waddington D" first="David" last="Waddington">David Waddington</name><affiliation><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff></affiliation></author><author><name sortKey="Watson, Michael" sort="Watson, Michael" uniqKey="Watson M" first="Michael" last="Watson">Michael Watson</name><affiliation><nlm:aff id="I14">Informatics Group, Institute for Animal Health, Compton, Newbury, Berks RG20 7NN, UK</nlm:aff></affiliation></author><author><name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name><affiliation><nlm:aff id="I13">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff></affiliation></author><author><name sortKey="Zerbe, Holm" sort="Zerbe, Holm" uniqKey="Zerbe H" first="Holm" last="Zerbe">Holm Zerbe</name><affiliation><nlm:aff id="I10">Clinic for Ruminants, Ludwig-Maximilians-University, Munich, Germany</nlm:aff></affiliation></author></analytic><series><title level="j">Genetics, Selection, Evolution : GSE</title><idno type="ISSN">0999-193X</idno><idno type="eISSN">1297-9686</idno><imprint><date when="2007">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The aim of this paper was to describe, and when possible compare, the multivariate methods used by the participants in the EADGENE WP1.4 workshop. The first approach was for class discovery and class prediction using evidence from the data at hand. Several teams used hierarchical clustering (HC) or principal component analysis (PCA) to identify groups of differentially expressed genes with a similar expression pattern over time points and infective agent (<italic>E. coli </italic>or <italic>S. aureus</italic>). The main result from these analyses was that HC and PCA were able to separate tissue samples taken at 24 h following <italic>E. coli </italic>infection from the other samples. The second approach identified groups of differentially co-expressed genes, by identifying clusters of genes highly correlated when animals were infected with <italic>E. coli </italic>but not correlated more than expected by chance when the infective pathogen was <italic>S. aureus</italic>. The third approach looked at differential expression of predefined gene sets. Gene sets were defined based on information retrieved from biological databases such as Gene Ontology. Based on these annotation sources the teams used either the GlobalTest or the Fisher exact test to identify differentially expressed gene sets. The main result from these analyses was that gene sets involved in immune defence responses were differentially expressed.</p></div></front></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genet Sel Evol</journal-id><journal-title>Genetics, Selection, Evolution : GSE</journal-title><issn pub-type="ppub">0999-193X</issn><issn pub-type="epub">1297-9686</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">18053574</article-id><article-id pub-id-type="pmc">2682812</article-id><article-id pub-id-type="publisher-id">1297-9686-39-6-651</article-id><article-id pub-id-type="doi">10.1186/1297-9686-39-6-651</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Analysis of the real EADGENE data set: Multivariate approaches and post analysis (<italic>Open Access publication</italic>)</article-title></title-group><contrib-group><contrib id="A1" corresp="yes" contrib-type="author"><name><surname>Sørensen</surname><given-names>Peter</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>pso@agrsci.dk</email></contrib><contrib id="A2" contrib-type="author"><name><surname>Bonnet</surname><given-names>Agnès</given-names></name><xref ref-type="aff" rid="I2">2</xref></contrib><contrib id="A3" contrib-type="author"><name><surname>Buitenhuis</surname><given-names>Bart</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A4" contrib-type="author"><name><surname>Closset</surname><given-names>Rodrigue</given-names></name><xref ref-type="aff" rid="I3">3</xref></contrib><contrib id="A5" contrib-type="author"><name><surname>Déjean</surname><given-names>Sébastien</given-names></name><xref ref-type="aff" rid="I4">4</xref></contrib><contrib id="A6" contrib-type="author"><name><surname>Delmas</surname><given-names>Céline</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A7" contrib-type="author"><name><surname>Duval</surname><given-names>Mylène</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A8" contrib-type="author"><name><surname>Glass</surname><given-names>Liz</given-names></name><xref ref-type="aff" rid="I6">6</xref></contrib><contrib id="A9" contrib-type="author"><name><surname>Hedegaard</surname><given-names>Jakob</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A10" contrib-type="author"><name><surname>Hornshøj</surname><given-names>Henrik</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A11" contrib-type="author"><name><surname>Hulsegge</surname><given-names>Ina</given-names></name><xref ref-type="aff" rid="I7">7</xref></contrib><contrib id="A12" contrib-type="author"><name><surname>Jaffrézic</surname><given-names>Florence</given-names></name><xref ref-type="aff" rid="I8">8</xref></contrib><contrib id="A13" contrib-type="author"><name><surname>Jensen</surname><given-names>Kirsty</given-names></name><xref ref-type="aff" rid="I6">6</xref></contrib><contrib id="A14" contrib-type="author"><name><surname>Jiang</surname><given-names>Li</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A15" contrib-type="author"><name><surname>de Koning</surname><given-names>Dirk-Jan</given-names></name><xref ref-type="aff" rid="I6">6</xref></contrib><contrib id="A16" contrib-type="author"><name><surname>Cao</surname><given-names>Kim-Anh Lê</given-names></name><xref ref-type="aff" rid="I4">4</xref><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A17" contrib-type="author"><name><surname>Nie</surname><given-names>Haisheng</given-names></name><xref ref-type="aff" rid="I9">9</xref></contrib><contrib id="A18" contrib-type="author"><name><surname>Petzl</surname><given-names>Wolfram</given-names></name><xref ref-type="aff" rid="I10">10</xref></contrib><contrib id="A19" contrib-type="author"><name><surname>Pool</surname><given-names>Marco H</given-names></name><xref ref-type="aff" rid="I7">7</xref></contrib><contrib id="A20" contrib-type="author"><name><surname>Robert-Granié</surname><given-names>Christèle</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A21" contrib-type="author"><name><surname>San Cristobal</surname><given-names>Magali</given-names></name><xref ref-type="aff" rid="I2">2</xref></contrib><contrib id="A22" contrib-type="author"><name><surname>Lund</surname><given-names>Mogens Sandø</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A23" contrib-type="author"><name><surname>van Schothorst</surname><given-names>Evert M</given-names></name><xref ref-type="aff" rid="I11">11</xref></contrib><contrib id="A24" contrib-type="author"><name><surname>Schuberth</surname><given-names>Hans-Joachim</given-names></name><xref ref-type="aff" rid="I12">12</xref></contrib><contrib id="A25" contrib-type="author"><name><surname>Seyfert</surname><given-names>Hans-Martin</given-names></name><xref ref-type="aff" rid="I13">13</xref></contrib><contrib id="A26" contrib-type="author"><name><surname>Tosser-Klopp</surname><given-names>Gwenola</given-names></name><xref ref-type="aff" rid="I12">12</xref></contrib><contrib id="A27" contrib-type="author"><name><surname>Waddington</surname><given-names>David</given-names></name><xref ref-type="aff" rid="I6">6</xref></contrib><contrib id="A28" contrib-type="author"><name><surname>Watson</surname><given-names>Michael</given-names></name><xref ref-type="aff" rid="I14">14</xref></contrib><contrib id="A29" contrib-type="author"><name><surname>Yang</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="I13">13</xref></contrib><contrib id="A30" contrib-type="author"><name><surname>Zerbe</surname><given-names>Holm</given-names></name><xref ref-type="aff" rid="I10">10</xref></contrib></contrib-group><aff id="I1"><label>1</label>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark</aff><aff id="I2"><label>2</label>INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan, France</aff><aff id="I3"><label>3</label>Faculty of Veterinary Medicine, University of Liege, Liege, Belgium</aff><aff id="I4"><label>4</label>Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse, France</aff><aff id="I5"><label>5</label>INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</aff><aff id="I6"><label>6</label>Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</aff><aff id="I7"><label>7</label>Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</aff><aff id="I8"><label>8</label>INRA, UR337 Station de génétique quantitative et appliquée, Jouy-en-Josas, 78350, France</aff><aff id="I9"><label>9</label>Animal Breeding and Genomics Centre, Wageningen University and Research Centre, The Netherlands</aff><aff id="I10"><label>10</label>Clinic for Ruminants, Ludwig-Maximilians-University, Munich, Germany</aff><aff id="I11"><label>11</label>Food Bioactives Group, RIKILT-Institute of Food Safety, Wageningen University and Research Centre, Wageningen, The Netherlands</aff><aff id="I12"><label>12</label>Immunology Unit, University of Veterinary Medicine, Hannover, Germany</aff><aff id="I13"><label>13</label>Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</aff><aff id="I14"><label>14</label>Informatics Group, Institute for Animal Health, Compton, Newbury, Berks RG20 7NN, UK</aff><pub-date pub-type="collection"><year>2007</year></pub-date><pub-date pub-type="epub"><day>15</day><month>11</month><year>2007</year></pub-date><volume>39</volume><issue>6</issue><fpage>651</fpage><lpage>668</lpage><ext-link ext-link-type="uri" xlink:href="http://www.gse-journal.org/content/39/6/651"></ext-link><history><date date-type="received"><day>10</day><month>5</month><year>2007</year></date><date date-type="accepted"><day>4</day><month>7</month><year>2007</year></date></history><permissions><copyright-statement>Copyright © 2007 INRA, EDP Sciences</copyright-statement><copyright-year>2007</copyright-year><copyright-holder>INRA, EDP Sciences</copyright-holder></permissions><abstract><p>The aim of this paper was to describe, and when possible compare, the multivariate methods used by the participants in the EADGENE WP1.4 workshop. The first approach was for class discovery and class prediction using evidence from the data at hand. Several teams used hierarchical clustering (HC) or principal component analysis (PCA) to identify groups of differentially expressed genes with a similar expression pattern over time points and infective agent (<italic>E. coli </italic>or <italic>S. aureus</italic>). The main result from these analyses was that HC and PCA were able to separate tissue samples taken at 24 h following <italic>E. coli </italic>infection from the other samples. The second approach identified groups of differentially co-expressed genes, by identifying clusters of genes highly correlated when animals were infected with <italic>E. coli </italic>but not correlated more than expected by chance when the infective pathogen was <italic>S. aureus</italic>. The third approach looked at differential expression of predefined gene sets. Gene sets were defined based on information retrieved from biological databases such as Gene Ontology. Based on these annotation sources the teams used either the GlobalTest or the Fisher exact test to identify differentially expressed gene sets. The main result from these analyses was that gene sets involved in immune defence responses were differentially expressed.</p></abstract><kwd-group><kwd>bovine annotation</kwd><kwd>bovine microarray</kwd><kwd>gene set analysis</kwd><kwd>mastitis</kwd><kwd>multivariate approaches</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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