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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (<italic>Open Access publication</italic>)</title><author><name sortKey="Jaffrezic, Florence" sort="Jaffrezic, Florence" uniqKey="Jaffrezic F" first="Florence" last="Jaffrézic">Florence Jaffrézic</name><affiliation><nlm:aff id="I1">INRA, UR337, Jouy-en-Josas, France (INRA_J)</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="I2">Roslin Institute, Roslin, UK (ROSLIN)</nlm:aff></affiliation></author><author><name sortKey="Boettcher, Paul J" sort="Boettcher, Paul J" uniqKey="Boettcher P" first="Paul J" last="Boettcher">Paul J. Boettcher</name><affiliation><nlm:aff id="I3">Parco Tecnologico Padano, Lodi, Italy (PTP)</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="I4">INRA, UMR444, Castanet-Tolosan, France (INRA_T)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</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="I6">University of Liège, Liège, Belgium (ULg2)</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="I7">Université Paul Sabatier, Toulouse, France (INRA_T)</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="I8">INRA, UR631, Castanet-Tolosan, France (INRA_T)</nlm:aff></affiliation></author><author><name sortKey="Detilleux, Johanne C" sort="Detilleux, Johanne C" uniqKey="Detilleux J" first="Johanne C" last="Detilleux">Johanne C. Detilleux</name><affiliation><nlm:aff id="I9">Faculty of Veterinary Medicine, University of Liège, Liège, Belgium (ULg1)</nlm:aff></affiliation></author><author><name sortKey="Dov, Peter" sort="Dov, Peter" uniqKey="Dov P" first="Peter" last="Dov">Peter Dov</name><affiliation><nlm:aff id="I10">University of Ljubljana, Slovenia (SLN)</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="I8">INRA, UR631, Castanet-Tolosan, France (INRA_T)</nlm:aff></affiliation></author><author><name sortKey="Foulley, Jean Louis" sort="Foulley, Jean Louis" uniqKey="Foulley J" first="Jean-Louis" last="Foulley">Jean-Louis Foulley</name><affiliation><nlm:aff id="I1">INRA, UR337, Jouy-en-Josas, France (INRA_J)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</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="I11">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Janss, Luc" sort="Janss, Luc" uniqKey="Janss L" first="Luc" last="Janss">Luc Janss</name><affiliation><nlm:aff id="I5">University of Aarhus, Tjele, Denmark (AARHUS)</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="I2">Roslin Institute, Roslin, UK (ROSLIN)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</nlm:aff></affiliation></author><author><name sortKey="Lavri, Miha" sort="Lavri, Miha" uniqKey="Lavri M" first="Miha" last="Lavri">Miha Lavri</name><affiliation><nlm:aff id="I10">University of Ljubljana, Slovenia (SLN)</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="I7">Université Paul Sabatier, Toulouse, France (INRA_T)</nlm:aff></affiliation><affiliation><nlm:aff id="I8">INRA, UR631, Castanet-Tolosan, France (INRA_T)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</nlm:aff></affiliation></author><author><name sortKey="Malinverni, Roberto" sort="Malinverni, Roberto" uniqKey="Malinverni R" first="Roberto" last="Malinverni">Roberto Malinverni</name><affiliation><nlm:aff id="I3">Parco Tecnologico Padano, Lodi, Italy (PTP)</nlm:aff></affiliation></author><author><name sortKey="Marot, Guillemette" sort="Marot, Guillemette" uniqKey="Marot G" first="Guillemette" last="Marot">Guillemette Marot</name><affiliation><nlm:aff id="I1">INRA, UR337, Jouy-en-Josas, France (INRA_J)</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="I12">Wageningen University and Research Centre, Wageningen, The Netherlands (WUR)</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="I13">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="I11">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="I8">INRA, UR631, Castanet-Tolosan, France (INRA_T)</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="I4">INRA, UMR444, Castanet-Tolosan, France (INRA_T)</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="I14">RIKILT-Institute of Food Safety, Wageningen, The Netherlands (WUR)</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="I15">University of Veterinary Medicine, Hannover, Germany</nlm:aff></affiliation></author><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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</nlm:aff></affiliation></author><author><name sortKey="Stella, Alessandra" sort="Stella, Alessandra" uniqKey="Stella A" first="Alessandra" last="Stella">Alessandra Stella</name><affiliation><nlm:aff id="I3">Parco Tecnologico Padano, Lodi, Italy (PTP)</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="I4">INRA, UMR444, Castanet-Tolosan, France (INRA_T)</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="I2">Roslin Institute, Roslin, UK (ROSLIN)</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="I16">Institute for Animal Health, Compton, UK (IAH)</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="I17">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="I13">Ludwig-Maximilians-University, Munich, 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="I17">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18053573</idno><idno type="pmc">2682811</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682811</idno><idno type="RBID">PMC:2682811</idno><idno type="doi">10.1186/1297-9686-39-6-633</idno><date when="2007">2007</date><idno type="wicri:Area/Pmc/Corpus">000235</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (<italic>Open Access publication</italic>)</title><author><name sortKey="Jaffrezic, Florence" sort="Jaffrezic, Florence" uniqKey="Jaffrezic F" first="Florence" last="Jaffrézic">Florence Jaffrézic</name><affiliation><nlm:aff id="I1">INRA, UR337, Jouy-en-Josas, France (INRA_J)</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="I2">Roslin Institute, Roslin, UK (ROSLIN)</nlm:aff></affiliation></author><author><name sortKey="Boettcher, Paul J" sort="Boettcher, Paul J" uniqKey="Boettcher P" first="Paul J" last="Boettcher">Paul J. Boettcher</name><affiliation><nlm:aff id="I3">Parco Tecnologico Padano, Lodi, Italy (PTP)</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="I4">INRA, UMR444, Castanet-Tolosan, France (INRA_T)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</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="I6">University of Liège, Liège, Belgium (ULg2)</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="I7">Université Paul Sabatier, Toulouse, France (INRA_T)</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="I8">INRA, UR631, Castanet-Tolosan, France (INRA_T)</nlm:aff></affiliation></author><author><name sortKey="Detilleux, Johanne C" sort="Detilleux, Johanne C" uniqKey="Detilleux J" first="Johanne C" last="Detilleux">Johanne C. Detilleux</name><affiliation><nlm:aff id="I9">Faculty of Veterinary Medicine, University of Liège, Liège, Belgium (ULg1)</nlm:aff></affiliation></author><author><name sortKey="Dov, Peter" sort="Dov, Peter" uniqKey="Dov P" first="Peter" last="Dov">Peter Dov</name><affiliation><nlm:aff id="I10">University of Ljubljana, Slovenia (SLN)</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="I8">INRA, UR631, Castanet-Tolosan, France (INRA_T)</nlm:aff></affiliation></author><author><name sortKey="Foulley, Jean Louis" sort="Foulley, Jean Louis" uniqKey="Foulley J" first="Jean-Louis" last="Foulley">Jean-Louis Foulley</name><affiliation><nlm:aff id="I1">INRA, UR337, Jouy-en-Josas, France (INRA_J)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</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="I11">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Janss, Luc" sort="Janss, Luc" uniqKey="Janss L" first="Luc" last="Janss">Luc Janss</name><affiliation><nlm:aff id="I5">University of Aarhus, Tjele, Denmark (AARHUS)</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="I2">Roslin Institute, Roslin, UK (ROSLIN)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</nlm:aff></affiliation></author><author><name sortKey="Lavri, Miha" sort="Lavri, Miha" uniqKey="Lavri M" first="Miha" last="Lavri">Miha Lavri</name><affiliation><nlm:aff id="I10">University of Ljubljana, Slovenia (SLN)</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="I7">Université Paul Sabatier, Toulouse, France (INRA_T)</nlm:aff></affiliation><affiliation><nlm:aff id="I8">INRA, UR631, Castanet-Tolosan, France (INRA_T)</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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</nlm:aff></affiliation></author><author><name sortKey="Malinverni, Roberto" sort="Malinverni, Roberto" uniqKey="Malinverni R" first="Roberto" last="Malinverni">Roberto Malinverni</name><affiliation><nlm:aff id="I3">Parco Tecnologico Padano, Lodi, Italy (PTP)</nlm:aff></affiliation></author><author><name sortKey="Marot, Guillemette" sort="Marot, Guillemette" uniqKey="Marot G" first="Guillemette" last="Marot">Guillemette Marot</name><affiliation><nlm:aff id="I1">INRA, UR337, Jouy-en-Josas, France (INRA_J)</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="I12">Wageningen University and Research Centre, Wageningen, The Netherlands (WUR)</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="I13">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="I11">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="I8">INRA, UR631, Castanet-Tolosan, France (INRA_T)</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="I4">INRA, UMR444, Castanet-Tolosan, France (INRA_T)</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="I14">RIKILT-Institute of Food Safety, Wageningen, The Netherlands (WUR)</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="I15">University of Veterinary Medicine, Hannover, Germany</nlm:aff></affiliation></author><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="I5">University of Aarhus, Tjele, Denmark (AARHUS)</nlm:aff></affiliation></author><author><name sortKey="Stella, Alessandra" sort="Stella, Alessandra" uniqKey="Stella A" first="Alessandra" last="Stella">Alessandra Stella</name><affiliation><nlm:aff id="I3">Parco Tecnologico Padano, Lodi, Italy (PTP)</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="I4">INRA, UMR444, Castanet-Tolosan, France (INRA_T)</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="I2">Roslin Institute, Roslin, UK (ROSLIN)</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="I16">Institute for Animal Health, Compton, UK (IAH)</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="I17">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="I13">Ludwig-Maximilians-University, Munich, 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="I17">Research Institute for the Biology of Farm Animals, Dummerstorf, 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>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: <italic>Escherichia coli </italic>and <italic>Staphylococcus aureus</italic>. 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 <italic>E. coli </italic>between uninfected and 24 h challenged udder quarters. Very little transcriptional variation was observed for the bacteria <italic>S. aureus</italic>. 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.</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">18053573</article-id><article-id pub-id-type="pmc">2682811</article-id><article-id pub-id-type="publisher-id">1297-9686-39-6-633</article-id><article-id pub-id-type="doi">10.1186/1297-9686-39-6-633</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: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (<italic>Open Access publication</italic>)</article-title></title-group><contrib-group><contrib id="A1" corresp="yes" contrib-type="author"><name><surname>Jaffrézic</surname><given-names>Florence</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>florence.jaffrezic@jouy.inra.fr</email></contrib><contrib id="A2" contrib-type="author"><name><surname>de Koning</surname><given-names>Dirk-Jan</given-names></name><xref ref-type="aff" rid="I2">2</xref></contrib><contrib id="A3" contrib-type="author"><name><surname>Boettcher</surname><given-names>Paul J</given-names></name><xref ref-type="aff" rid="I3">3</xref></contrib><contrib id="A4" contrib-type="author"><name><surname>Bonnet</surname><given-names>Agnès</given-names></name><xref ref-type="aff" rid="I4">4</xref></contrib><contrib id="A5" contrib-type="author"><name><surname>Buitenhuis</surname><given-names>Bart</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A6" contrib-type="author"><name><surname>Closset</surname><given-names>Rodrigue</given-names></name><xref ref-type="aff" rid="I6">6</xref></contrib><contrib id="A7" contrib-type="author"><name><surname>Déjean</surname><given-names>Sébastien</given-names></name><xref ref-type="aff" rid="I7">7</xref></contrib><contrib id="A8" contrib-type="author"><name><surname>Delmas</surname><given-names>Céline</given-names></name><xref ref-type="aff" rid="I8">8</xref></contrib><contrib id="A9" contrib-type="author"><name><surname>Detilleux</surname><given-names>Johanne C</given-names></name><xref ref-type="aff" rid="I9">9</xref></contrib><contrib id="A10" contrib-type="author"><name><surname>Dovč</surname><given-names>Peter</given-names></name><xref ref-type="aff" rid="I10">10</xref></contrib><contrib id="A11" contrib-type="author"><name><surname>Duval</surname><given-names>Mylène</given-names></name><xref ref-type="aff" rid="I8">8</xref></contrib><contrib id="A12" contrib-type="author"><name><surname>Foulley</surname><given-names>Jean-Louis</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A13" contrib-type="author"><name><surname>Hedegaard</surname><given-names>Jakob</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A14" contrib-type="author"><name><surname>Hornshøj</surname><given-names>Henrik</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A15" contrib-type="author"><name><surname>Hulsegge</surname><given-names>Ina</given-names></name><xref ref-type="aff" rid="I11">11</xref></contrib><contrib id="A16" contrib-type="author"><name><surname>Janss</surname><given-names>Luc</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A17" contrib-type="author"><name><surname>Jensen</surname><given-names>Kirsty</given-names></name><xref ref-type="aff" rid="I2">2</xref></contrib><contrib id="A18" contrib-type="author"><name><surname>Jiang</surname><given-names>Li</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A19" contrib-type="author"><name><surname>Lavrič</surname><given-names>Miha</given-names></name><xref ref-type="aff" rid="I10">10</xref></contrib><contrib id="A20" contrib-type="author"><name><surname>Cao</surname><given-names>Kim-Anh Lê</given-names></name><xref ref-type="aff" rid="I7">7</xref><xref ref-type="aff" rid="I8">8</xref></contrib><contrib id="A21" contrib-type="author"><name><surname>Lund</surname><given-names>Mogens Sandø</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A22" contrib-type="author"><name><surname>Malinverni</surname><given-names>Roberto</given-names></name><xref ref-type="aff" rid="I3">3</xref></contrib><contrib id="A23" contrib-type="author"><name><surname>Marot</surname><given-names>Guillemette</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A24" contrib-type="author"><name><surname>Nie</surname><given-names>Haisheng</given-names></name><xref ref-type="aff" rid="I12">12</xref></contrib><contrib id="A25" contrib-type="author"><name><surname>Petzl</surname><given-names>Wolfram</given-names></name><xref ref-type="aff" rid="I13">13</xref></contrib><contrib id="A26" contrib-type="author"><name><surname>Pool</surname><given-names>Marco H</given-names></name><xref ref-type="aff" rid="I11">11</xref></contrib><contrib id="A27" contrib-type="author"><name><surname>Robert-Granié</surname><given-names>Christèle</given-names></name><xref ref-type="aff" rid="I8">8</xref></contrib><contrib id="A28" contrib-type="author"><name><surname>San Cristobal</surname><given-names>Magali</given-names></name><xref ref-type="aff" rid="I4">4</xref></contrib><contrib id="A29" contrib-type="author"><name><surname>van Schothorst</surname><given-names>Evert M</given-names></name><xref ref-type="aff" rid="I14">14</xref></contrib><contrib id="A30" contrib-type="author"><name><surname>Schuberth</surname><given-names>Hans-Joachim</given-names></name><xref ref-type="aff" rid="I15">15</xref></contrib><contrib id="A31" contrib-type="author"><name><surname>Sørensen</surname><given-names>Peter</given-names></name><xref ref-type="aff" rid="I5">5</xref></contrib><contrib id="A32" contrib-type="author"><name><surname>Stella</surname><given-names>Alessandra</given-names></name><xref ref-type="aff" rid="I3">3</xref></contrib><contrib id="A33" contrib-type="author"><name><surname>Tosser-Klopp</surname><given-names>Gwenola</given-names></name><xref ref-type="aff" rid="I4">4</xref></contrib><contrib id="A34" contrib-type="author"><name><surname>Waddington</surname><given-names>David</given-names></name><xref ref-type="aff" rid="I2">2</xref></contrib><contrib id="A35" contrib-type="author"><name><surname>Watson</surname><given-names>Michael</given-names></name><xref ref-type="aff" rid="I16">16</xref></contrib><contrib id="A36" contrib-type="author"><name><surname>Yang</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="I17">17</xref></contrib><contrib id="A37" contrib-type="author"><name><surname>Zerbe</surname><given-names>Holm</given-names></name><xref ref-type="aff" rid="I13">13</xref></contrib><contrib id="A38" contrib-type="author"><name><surname>Seyfert</surname><given-names>Hans-Martin</given-names></name><xref ref-type="aff" rid="I17">17</xref></contrib></contrib-group><aff id="I1"><label>1</label>INRA, UR337, Jouy-en-Josas, France (INRA_J)</aff><aff id="I2"><label>2</label>Roslin Institute, Roslin, UK (ROSLIN)</aff><aff id="I3"><label>3</label>Parco Tecnologico Padano, Lodi, Italy (PTP)</aff><aff id="I4"><label>4</label>INRA, UMR444, Castanet-Tolosan, France (INRA_T)</aff><aff id="I5"><label>5</label>University of Aarhus, Tjele, Denmark (AARHUS)</aff><aff id="I6"><label>6</label>University of Liège, Liège, Belgium (ULg2)</aff><aff id="I7"><label>7</label>Université Paul Sabatier, Toulouse, France (INRA_T)</aff><aff id="I8"><label>8</label>INRA, UR631, Castanet-Tolosan, France (INRA_T)</aff><aff id="I9"><label>9</label>Faculty of Veterinary Medicine, University of Liège, Liège, Belgium (ULg1)</aff><aff id="I10"><label>10</label>University of Ljubljana, Slovenia (SLN)</aff><aff id="I11"><label>11</label>Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</aff><aff id="I12"><label>12</label>Wageningen University and Research Centre, Wageningen, The Netherlands (WUR)</aff><aff id="I13"><label>13</label>Ludwig-Maximilians-University, Munich, Germany</aff><aff id="I14"><label>14</label>RIKILT-Institute of Food Safety, Wageningen, The Netherlands (WUR)</aff><aff id="I15"><label>15</label>University of Veterinary Medicine, Hannover, Germany</aff><aff id="I16"><label>16</label>Institute for Animal Health, Compton, UK (IAH)</aff><aff id="I17"><label>17</label>Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</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>633</fpage><lpage>650</lpage><ext-link ext-link-type="uri" xlink:href="http://www.gse-journal.org/content/39/6/633"></ext-link><history><date date-type="received"><day>10</day><month>5</month><year>2007</year></date><date date-type="accepted"><day>6</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>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: <italic>Escherichia coli </italic>and <italic>Staphylococcus aureus</italic>. 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 <italic>E. coli </italic>between uninfected and 24 h challenged udder quarters. Very little transcriptional variation was observed for the bacteria <italic>S. aureus</italic>. 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.</p></abstract><kwd-group><kwd>quality control</kwd><kwd>differentially expressed genes</kwd><kwd>mastitis resistance</kwd><kwd>microarray data</kwd><kwd>normalisation</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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