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 Netherlands

12-14 November 2008

  1. Research

    Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis

    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...

    Pieter BT Neerincx, Pierrot Casel, Dennis Prickett, Haisheng Nie, Michael Watson, Jack AM Leunissen, Martien AM Groenen and Christophe Klopp

    BMC Proceedings 2009 3(Suppl 4):S1

    Published on: 16 July 2009

  2. Research

    IMAD: flexible annotation of microarray sequences

    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...

    Dennis Prickett and Michael Watson

    BMC Proceedings 2009 3(Suppl 4):S2

    Published on: 16 July 2009

  3. Research

    OligoRAP – an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity

    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...

    Pieter BT Neerincx, Han Rauwerda, Haisheng Nie, Martien AM Groenen, Timo M Breit and Jack AM Leunissen

    BMC Proceedings 2009 3(Suppl 4):S4

    Published on: 16 July 2009

  4. Research

    Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

    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...

    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…

    BMC Proceedings 2009 3(Suppl 4):S5

    Published on: 16 July 2009

  5. Research

    Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis

    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...

    Ángeles Jiménez-Marín, Melania Collado-Romero, María Ramirez-Boo, Cristina Arce and Juan J Garrido

    BMC Proceedings 2009 3(Suppl 4):S6

    Published on: 16 July 2009

  6. Research

    Gene set analysis methods applied to chicken microarray expression data

    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...

    Axel Skarman, Li Jiang, Henrik Hornshøj, Bart Buitenhuis, Jakob Hedegaard, Lene N Conley and Peter Sørensen

    BMC Proceedings 2009 3(Suppl 4):S8

    Published on: 16 July 2009

  7. Research

    Microarray data mining using Bioconductor packages

    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-...

    Haisheng Nie, Pieter BT Neerincx, Jan van der Poel, Francesco Ferrari, Silvio Bicciato, Jack AM Leunissen and Martien AM Groenen

    BMC Proceedings 2009 3(Suppl 4):S9

    Published on: 16 July 2009

  8. Research

    Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares

    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...

    Agnès Bonnet, Sandrine Lagarrigue, Laurence Liaubet, Christèle Robert-Granié, Magali SanCristobal and Gwenola Tosser-Klopp

    BMC Proceedings 2009 3(Suppl 4):S11

    Published on: 16 July 2009

  9. Research

    Gene network reconstruction from microarray data

    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...

    Florence Jaffrezic and Gwenola Tosser-Klopp

    BMC Proceedings 2009 3(Suppl 4):S12

    Published on: 16 July 2009

  10. Research

    Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs

    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 ...

    Vincent Jouffe, Suzanne Rowe, Laurence Liaubet, Bart Buitenhuis, Henrik Hornshøj, Magali SanCristobal, Pierre Mormède and DJ de Koning

    BMC Proceedings 2009 3(Suppl 4):S14

    Published on: 16 July 2009