Analysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication)
Identifieur interne : 001441 ( Main/Merge ); précédent : 001440; suivant : 001442Analysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication)
Auteurs : Peter S Rensen [Danemark] ; Agnès Bonnet [France] ; Bart Buitenhuis [Danemark] ; Rodrigue Closset [Belgique] ; Sébastien Déjean [France] ; Céline Delmas [France] ; Mylène Duval [France] ; Liz Glass [Royaume-Uni] ; Jakob Hedegaard [Danemark] ; Henrik Hornsh J [Danemark] ; Ina Hulsegge [Pays-Bas] ; Florence Jaffrézic [France] ; Kirsty Jensen [Royaume-Uni] ; Li Jiang [Danemark] ; Dirk-Jan De Koning [Royaume-Uni] ; Kim-Anh Lê Cao [France] ; Haisheng Nie [Pays-Bas] ; Wolfram Petzl [Allemagne] ; Marco H. Pool [Pays-Bas] ; Christèle Robert-Granié [France] ; Magali San Cristobal [France] ; Mogens Sand Lund [Danemark] ; Evert M. Van Schothorst [Pays-Bas] ; Hans-Joachim Schuberth [Allemagne] ; Hans-Martin Seyfert [Allemagne] ; Gwenola Tosser-Klopp [Allemagne] ; David Waddington [Royaume-Uni] ; Michael Watson [Royaume-Uni] ; Wei Yang [Allemagne] ; Holm Zerbe [Allemagne]Source :
- Genetics, Selection, Evolution : GSE [ 0999-193X ] ; 2007.
Abstract
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 (
Url:
DOI: 10.1186/1297-9686-39-6-651
PubMed: 18053574
PubMed Central: 2682812
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Box 50 DK-8830 Tjele, Denmark</nlm:aff><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></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 wicri:level="1"><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><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></affiliation></author><author><name sortKey="Hulsegge, Ina" sort="Hulsegge, Ina" uniqKey="Hulsegge I" first="Ina" last="Hulsegge">Ina Hulsegge</name><affiliation wicri:level="1"><nlm:aff id="I7">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Animal Sciences Group Wageningen UR, Lelystad</wicri:regionArea><wicri:noRegion>Lelystad</wicri:noRegion></affiliation></author><author><name sortKey="Jaffrezic, Florence" sort="Jaffrezic, Florence" uniqKey="Jaffrezic F" first="Florence" last="Jaffrézic">Florence Jaffrézic</name><affiliation wicri:level="3"><nlm:aff id="I8">INRA, UR337 Station de génétique quantitative et appliquée, Jouy-en-Josas, 78350, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR337 Station de génétique quantitative et appliquée, Jouy-en-Josas, 78350</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Jensen, Kirsty" sort="Jensen, Kirsty" uniqKey="Jensen K" first="Kirsty" last="Jensen">Kirsty Jensen</name><affiliation wicri:level="1"><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff><country>Royaume-Uni</country><wicri:regionArea>Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS</wicri:regionArea><wicri:noRegion>EH25 9PS</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Li" sort="Jiang, Li" uniqKey="Jiang L" first="Li" last="Jiang">Li Jiang</name><affiliation wicri:level="1"><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><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></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 wicri:level="1"><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff><country>Royaume-Uni</country><wicri:regionArea>Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS</wicri:regionArea><wicri:noRegion>EH25 9PS</wicri:noRegion></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 wicri:level="4"><nlm:aff id="I4">Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Toulouse</settlement></placeName><orgName type="university">Université Toulouse III - Paul Sabatier</orgName></affiliation><affiliation wicri:level="3"><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Castanet-Tolosan</settlement></placeName></affiliation></author><author><name sortKey="Nie, Haisheng" sort="Nie, Haisheng" uniqKey="Nie H" first="Haisheng" last="Nie">Haisheng Nie</name><affiliation wicri:level="1"><nlm:aff id="I9">Animal Breeding and Genomics Centre, Wageningen University and Research Centre, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Animal Breeding and Genomics Centre, Wageningen University and Research Centre</wicri:regionArea><wicri:noRegion>Wageningen University and Research Centre</wicri:noRegion></affiliation></author><author><name sortKey="Petzl, Wolfram" sort="Petzl, Wolfram" uniqKey="Petzl W" first="Wolfram" last="Petzl">Wolfram Petzl</name><affiliation wicri:level="4"><nlm:aff id="I10">Clinic for Ruminants, Ludwig-Maximilians-University, Munich, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Clinic for Ruminants, Ludwig-Maximilians-University, Munich</wicri:regionArea><placeName><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Haute-Bavière</region><settlement type="city">Munich</settlement></placeName><orgName type="university">Université Louis-et-Maximilien de Munich</orgName></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 wicri:level="1"><nlm:aff id="I7">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Animal Sciences Group Wageningen UR, Lelystad</wicri:regionArea><wicri:noRegion>Lelystad</wicri:noRegion></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 wicri:level="3"><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Castanet-Tolosan</settlement></placeName></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 wicri:level="3"><nlm:aff id="I2">INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Castanet-Tolosan</settlement></placeName></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 wicri:level="1"><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><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></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 wicri:level="1"><nlm:aff id="I11">Food Bioactives Group, RIKILT-Institute of Food Safety, Wageningen University and Research Centre, Wageningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Food Bioactives Group, RIKILT-Institute of Food Safety, Wageningen University and Research Centre, Wageningen</wicri:regionArea><wicri:noRegion>Wageningen</wicri:noRegion></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 wicri:level="3"><nlm:aff id="I12">Immunology Unit, University of Veterinary Medicine, Hannover, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Immunology Unit, University of Veterinary Medicine, Hannover</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Hanovre</settlement></placeName></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 wicri:level="1"><nlm:aff id="I13">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Research Institute for the Biology of Farm Animals, Dummerstorf</wicri:regionArea><wicri:noRegion>Dummerstorf</wicri:noRegion><wicri:noRegion>Dummerstorf</wicri:noRegion><wicri:noRegion>Dummerstorf</wicri:noRegion></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 wicri:level="3"><nlm:aff id="I12">Immunology Unit, University of Veterinary Medicine, Hannover, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Immunology Unit, University of Veterinary Medicine, Hannover</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Hanovre</settlement></placeName></affiliation></author><author><name sortKey="Waddington, David" sort="Waddington, David" uniqKey="Waddington D" first="David" last="Waddington">David Waddington</name><affiliation wicri:level="1"><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff><country>Royaume-Uni</country><wicri:regionArea>Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS</wicri:regionArea><wicri:noRegion>EH25 9PS</wicri:noRegion></affiliation></author><author><name sortKey="Watson, Michael" sort="Watson, Michael" uniqKey="Watson M" first="Michael" last="Watson">Michael Watson</name><affiliation wicri:level="1"><nlm:aff id="I14">Informatics Group, Institute for Animal Health, Compton, Newbury, Berks RG20 7NN, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Informatics Group, Institute for Animal Health, Compton, Newbury, Berks RG20 7NN</wicri:regionArea><wicri:noRegion>Berks RG20 7NN</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name><affiliation wicri:level="1"><nlm:aff id="I13">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Research Institute for the Biology of Farm Animals, Dummerstorf</wicri:regionArea><wicri:noRegion>Dummerstorf</wicri:noRegion><wicri:noRegion>Dummerstorf</wicri:noRegion><wicri:noRegion>Dummerstorf</wicri:noRegion></affiliation></author><author><name sortKey="Zerbe, Holm" sort="Zerbe, Holm" uniqKey="Zerbe H" first="Holm" last="Zerbe">Holm Zerbe</name><affiliation wicri:level="4"><nlm:aff id="I10">Clinic for Ruminants, Ludwig-Maximilians-University, Munich, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Clinic for Ruminants, Ludwig-Maximilians-University, Munich</wicri:regionArea><placeName><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Haute-Bavière</region><settlement type="city">Munich</settlement></placeName><orgName type="university">Université Louis-et-Maximilien de Munich</orgName></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><idno type="wicri:Area/Pmc/Curation">000236</idno><idno 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Box 50 DK-8830 Tjele, Denmark</nlm:aff><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></affiliation></author><author><name sortKey="Bonnet, Agnes" sort="Bonnet, Agnes" uniqKey="Bonnet A" first="Agnès" last="Bonnet">Agnès Bonnet</name><affiliation wicri:level="3"><nlm:aff id="I2">INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Castanet-Tolosan</settlement></placeName></affiliation></author><author><name sortKey="Buitenhuis, Bart" sort="Buitenhuis, Bart" uniqKey="Buitenhuis B" first="Bart" last="Buitenhuis">Bart Buitenhuis</name><affiliation wicri:level="1"><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><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></affiliation></author><author><name sortKey="Closset, Rodrigue" sort="Closset, Rodrigue" uniqKey="Closset R" first="Rodrigue" last="Closset">Rodrigue Closset</name><affiliation wicri:level="1"><nlm:aff id="I3">Faculty of Veterinary Medicine, University of Liege, Liege, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Faculty of Veterinary Medicine, University of Liege, Liege</wicri:regionArea><wicri:noRegion>Liege</wicri:noRegion></affiliation></author><author><name sortKey="Dejean, Sebastien" sort="Dejean, Sebastien" uniqKey="Dejean S" first="Sébastien" last="Déjean">Sébastien Déjean</name><affiliation wicri:level="4"><nlm:aff id="I4">Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Toulouse</settlement></placeName><orgName type="university">Université Toulouse III - Paul Sabatier</orgName></affiliation></author><author><name sortKey="Delmas, Celine" sort="Delmas, Celine" uniqKey="Delmas C" first="Céline" last="Delmas">Céline Delmas</name><affiliation wicri:level="3"><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Castanet-Tolosan</settlement></placeName></affiliation></author><author><name sortKey="Duval, Mylene" sort="Duval, Mylene" uniqKey="Duval M" first="Mylène" last="Duval">Mylène Duval</name><affiliation wicri:level="3"><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Castanet-Tolosan</settlement></placeName></affiliation></author><author><name sortKey="Glass, Liz" sort="Glass, Liz" uniqKey="Glass L" first="Liz" last="Glass">Liz Glass</name><affiliation wicri:level="1"><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff><country>Royaume-Uni</country><wicri:regionArea>Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS</wicri:regionArea><wicri:noRegion>EH25 9PS</wicri:noRegion></affiliation></author><author><name sortKey="Hedegaard, Jakob" sort="Hedegaard, Jakob" uniqKey="Hedegaard J" first="Jakob" last="Hedegaard">Jakob Hedegaard</name><affiliation wicri:level="1"><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><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></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 wicri:level="1"><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><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></affiliation></author><author><name sortKey="Hulsegge, Ina" sort="Hulsegge, Ina" uniqKey="Hulsegge I" first="Ina" last="Hulsegge">Ina Hulsegge</name><affiliation wicri:level="1"><nlm:aff id="I7">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Animal Sciences Group Wageningen UR, Lelystad</wicri:regionArea><wicri:noRegion>Lelystad</wicri:noRegion></affiliation></author><author><name sortKey="Jaffrezic, Florence" sort="Jaffrezic, Florence" uniqKey="Jaffrezic F" first="Florence" last="Jaffrézic">Florence Jaffrézic</name><affiliation wicri:level="3"><nlm:aff id="I8">INRA, UR337 Station de génétique quantitative et appliquée, Jouy-en-Josas, 78350, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR337 Station de génétique quantitative et appliquée, Jouy-en-Josas, 78350</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Jensen, Kirsty" sort="Jensen, Kirsty" uniqKey="Jensen K" first="Kirsty" last="Jensen">Kirsty Jensen</name><affiliation wicri:level="1"><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff><country>Royaume-Uni</country><wicri:regionArea>Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS</wicri:regionArea><wicri:noRegion>EH25 9PS</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Li" sort="Jiang, Li" uniqKey="Jiang L" first="Li" last="Jiang">Li Jiang</name><affiliation wicri:level="1"><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><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></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 wicri:level="1"><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff><country>Royaume-Uni</country><wicri:regionArea>Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS</wicri:regionArea><wicri:noRegion>EH25 9PS</wicri:noRegion></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 wicri:level="4"><nlm:aff id="I4">Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Université Paul Sabatier, UMR 5219 Laboratoire de statistique et probabilités, 31062 Toulouse</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Toulouse</settlement></placeName><orgName type="university">Université Toulouse III - Paul Sabatier</orgName></affiliation><affiliation wicri:level="3"><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Castanet-Tolosan</settlement></placeName></affiliation></author><author><name sortKey="Nie, Haisheng" sort="Nie, Haisheng" uniqKey="Nie H" first="Haisheng" last="Nie">Haisheng Nie</name><affiliation wicri:level="1"><nlm:aff id="I9">Animal Breeding and Genomics Centre, Wageningen University and Research Centre, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Animal Breeding and Genomics Centre, Wageningen University and Research Centre</wicri:regionArea><wicri:noRegion>Wageningen University and Research Centre</wicri:noRegion></affiliation></author><author><name sortKey="Petzl, Wolfram" sort="Petzl, Wolfram" uniqKey="Petzl W" first="Wolfram" last="Petzl">Wolfram Petzl</name><affiliation wicri:level="4"><nlm:aff id="I10">Clinic for Ruminants, Ludwig-Maximilians-University, Munich, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Clinic for Ruminants, Ludwig-Maximilians-University, Munich</wicri:regionArea><placeName><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Haute-Bavière</region><settlement type="city">Munich</settlement></placeName><orgName type="university">Université Louis-et-Maximilien de Munich</orgName></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 wicri:level="1"><nlm:aff id="I7">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Animal Sciences Group Wageningen UR, Lelystad</wicri:regionArea><wicri:noRegion>Lelystad</wicri:noRegion></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 wicri:level="3"><nlm:aff id="I5">INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR631 Station d'amélioration génétique des animaux, BP 52627, 31326 Castanet-Tolosan</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Castanet-Tolosan</settlement></placeName></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 wicri:level="3"><nlm:aff id="I2">INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UMR 444 Laboratoire de génétique cellulaire, BP 52627, 31326 Castanet-Tolosan</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Castanet-Tolosan</settlement></placeName></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 wicri:level="1"><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><country xml:lang="fr">Danemark</country><wicri:regionArea>University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele</wicri:regionArea><wicri:noRegion>P.O. Box 50 DK-8830 Tjele</wicri:noRegion></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 wicri:level="1"><nlm:aff id="I11">Food Bioactives Group, RIKILT-Institute of Food Safety, Wageningen University and Research Centre, Wageningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Food Bioactives Group, RIKILT-Institute of Food Safety, Wageningen University and Research Centre, Wageningen</wicri:regionArea><wicri:noRegion>Wageningen</wicri:noRegion></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 wicri:level="3"><nlm:aff id="I12">Immunology Unit, University of Veterinary Medicine, Hannover, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Immunology Unit, University of Veterinary Medicine, Hannover</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Hanovre</settlement></placeName></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 wicri:level="1"><nlm:aff id="I13">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Research Institute for the Biology of Farm Animals, Dummerstorf</wicri:regionArea><wicri:noRegion>Dummerstorf</wicri:noRegion><wicri:noRegion>Dummerstorf</wicri:noRegion><wicri:noRegion>Dummerstorf</wicri:noRegion></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 wicri:level="3"><nlm:aff id="I12">Immunology Unit, University of Veterinary Medicine, Hannover, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Immunology Unit, University of Veterinary Medicine, Hannover</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Hanovre</settlement></placeName></affiliation></author><author><name sortKey="Waddington, David" sort="Waddington, David" uniqKey="Waddington D" first="David" last="Waddington">David Waddington</name><affiliation wicri:level="1"><nlm:aff id="I6">Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK (RLN)</nlm:aff><country>Royaume-Uni</country><wicri:regionArea>Roslin Institute, Department of Genetics and Genomics, Roslin Biocentre, Roslin, Midlothian, EH25 9PS</wicri:regionArea><wicri:noRegion>EH25 9PS</wicri:noRegion></affiliation></author><author><name sortKey="Watson, Michael" sort="Watson, Michael" uniqKey="Watson M" first="Michael" last="Watson">Michael Watson</name><affiliation wicri:level="1"><nlm:aff id="I14">Informatics Group, Institute for Animal Health, Compton, Newbury, Berks RG20 7NN, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Informatics Group, Institute for Animal Health, Compton, Newbury, Berks RG20 7NN</wicri:regionArea><wicri:noRegion>Berks RG20 7NN</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name><affiliation wicri:level="1"><nlm:aff id="I13">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Research Institute for the Biology of Farm Animals, Dummerstorf</wicri:regionArea><wicri:noRegion>Dummerstorf</wicri:noRegion><wicri:noRegion>Dummerstorf</wicri:noRegion><wicri:noRegion>Dummerstorf</wicri:noRegion></affiliation></author><author><name sortKey="Zerbe, Holm" sort="Zerbe, Holm" uniqKey="Zerbe H" first="Holm" last="Zerbe">Holm Zerbe</name><affiliation wicri:level="4"><nlm:aff id="I10">Clinic for Ruminants, Ludwig-Maximilians-University, Munich, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Clinic for Ruminants, Ludwig-Maximilians-University, Munich</wicri:regionArea><placeName><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Haute-Bavière</region><settlement type="city">Munich</settlement></placeName><orgName type="university">Université Louis-et-Maximilien de Munich</orgName></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></record>Pour manipuler ce document sous Unix (Dilib)
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