This article is part of the supplement: EADGENE and SABRE Post-analyses Workshop

Open Access Research

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

Agnès Bonnet1, Sandrine Lagarrigue23, Laurence Liaubet1, Christèle Robert-Granié4, Magali SanCristobal1 and Gwenola Tosser-Klopp1*

Author Affiliations

1 INRA, UMR444, Laboratoire de Génétique Cellulaire, F-31326 Castanet-Tolosan, France

2 INRA, UMR 598, Génétique Animale, F-35000 Rennes, France

3 Agrocampus Ouest, UMR 598 Génétique Animale, F-35000 Rennes, France

4 INRA, UR631, Station d'Amélioration Génétique des Animaux, F-31326 Castanet-Tolosan, France

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BMC Proceedings 2009, 3(Suppl 4):S11  doi:10.1186/1753-6561-3-S4-S11

Published: 16 July 2009



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 results.


GOTM, Pathway Studio and Ingenuity softwares were used to investigate the three lists of genes. The three softwares allowed the analysis of the data and highlighted different networks. However, only one set of genes, showing a differential expression between primary and secondary response gave significant biological interpretation.


Combining these databases that were developed independently on different annotation sources supplies a useful tool for a global biological interpretation of microarray data, even if they may contain some imperfections (e.g. gene not or not well annotated).