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Volume 3 Supplement 4

EADGENE and SABRE Post-analyses Workshop


Edited by Dirk-Jan de Koning

The publication of these proceedings was supported by the EC-funded Network of Excellence EADGENE (EC contract number FOOD-CT-2004-506416).

EADGENE and SABRE Post-analyses Workshop. Go to conference site.

Lelystad, The Netherlands12-14 November 2008

  1. Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the a...

    Authors: Pieter BT Neerincx, Pierrot Casel, Dennis Prickett, Haisheng Nie, Michael Watson, Jack AM Leunissen, Martien AM Groenen and Christophe Klopp
    Citation: BMC Proceedings 2009 3(Suppl 4):S1
  2. Accurate and current functional annotation of microarray probes is essential for the analysis and interpretation of the biological processes involved. As gene structures and functional annotation are updated i...

    Authors: Dennis Prickett and Michael Watson
    Citation: BMC Proceedings 2009 3(Suppl 4):S2
  3. Microarray is a powerful technology enabling to monitor tens of thousands of genes in a single experiment. Most microarrays are now using oligo-sets. The design of the oligo-nucleotides is time consuming and e...

    Authors: Pierrot Casel, François Moreews, Sandrine Lagarrigue and Christophe Klopp
    Citation: BMC Proceedings 2009 3(Suppl 4):S3
  4. High throughput gene expression studies using oligonucleotide microarrays depend on the specificity of each oligonucleotide (oligo or probe) for its target gene. However, target specific probes can only be des...

    Authors: Pieter BT Neerincx, Han Rauwerda, Haisheng Nie, Martien AM Groenen, Timo M Breit and Jack AM Leunissen
    Citation: BMC Proceedings 2009 3(Suppl 4):S4
  5. The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edg...

    Authors: Jakob Hedegaard, Cristina Arce, Silvio Bicciato, Agnès Bonnet, Bart Buitenhuis, Melania Collado-Romero, Lene N Conley, Magali SanCristobal, Francesco Ferrari, Juan J Garrido, Martien AM Groenen, Henrik Hornshøj, Ina Hulsegge, Li Jiang, Ángeles Jiménez-Marín, Arun Kommadath…
    Citation: BMC Proceedings 2009 3(Suppl 4):S5
  6. Once a list of differentially expressed genes has been identified from a microarray experiment, a subsequent post-analysis task is required in order to find the main biological processes associated to the expe...

    Authors: Ángeles Jiménez-Marín, Melania Collado-Romero, María Ramirez-Boo, Cristina Arce and Juan J Garrido
    Citation: BMC Proceedings 2009 3(Suppl 4):S6
  7. Gene set analysis is considered to be a way of improving our biological interpretation of the observed expression patterns. This paper describes different methods applied to analyse expression data from a chic...

    Authors: Axel Skarman, Li Jiang, Henrik Hornshøj, Bart Buitenhuis, Jakob Hedegaard, Lene N Conley and Peter Sørensen
    Citation: BMC Proceedings 2009 3(Suppl 4):S8
  8. This paper describes the results of a Gene Ontology (GO) term enrichment analysis of chicken microarray data using the Bioconductor packages. By checking the enriched GO terms in three contrasts, MM8-PM8, MM8-...

    Authors: Haisheng Nie, Pieter BT Neerincx, Jan van der Poel, Francesco Ferrari, Silvio Bicciato, Jack AM Leunissen and Martien AM Groenen
    Citation: BMC Proceedings 2009 3(Suppl 4):S9
  9. As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these...

    Authors: Agnès Bonnet, Sandrine Lagarrigue, Laurence Liaubet, Christèle Robert-Granié, Magali SanCristobal and Gwenola Tosser-Klopp
    Citation: BMC Proceedings 2009 3(Suppl 4):S11
  10. Often, software available for biological pathways reconstruction rely on literature search to find links between genes. The aim of this study is to reconstruct gene networks from microarray data, using Graphic...

    Authors: Florence Jaffrezic and Gwenola Tosser-Klopp
    Citation: BMC Proceedings 2009 3(Suppl 4):S12
  11. Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a ...

    Authors: Vincent Jouffe, Suzanne Rowe, Laurence Liaubet, Bart Buitenhuis, Henrik Hornshøj, Magali SanCristobal, Pierre Mormède and DJ de Koning
    Citation: BMC Proceedings 2009 3(Suppl 4):S14

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