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

Open Access Highly Accessed Research

Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis

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

  • * Corresponding author: Juan J Garrido ge1gapaj@uco.es

  • † Equal contributors

Author Affiliations

Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Campus de Rabanales, Edificio C-5, 14071 Córdoba, Spain

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BMC Proceedings 2009, 3(Suppl 4):S6  doi:10.1186/1753-6561-3-S4-S6

Published: 16 July 2009

Abstract

Background

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 experimental system. This paper describes two pathways analysis tools, ArrayUnlock and Ingenuity Pathways Analysis (IPA) to deal with the post-analyses of microarray data, in the context of the EADGENE and SABRE post-analysis workshop. Dataset employed in this study proceeded from an experimental chicken infection performed to study the host reactions after a homologous or heterologous secondary challenge with two species of Eimeria.

Results

Analysis of the same microarray data source employing both commercial pathway analysis tools in parallel let to identify several biological and/or molecular functions altered in the chicken Eimeria maxima infection model, including several immune system related pathways. Biological functions differentially altered in the homologous and heterologous second infection were identified. Similarly, the effect of the timing in a homologous second infection was characterized by several biological functions.

Conclusion

Functional analysis with ArrayUnlock and IPA provided information related to functional differences with the three comparisons of the chicken infection leading to similar conclusions. ArrayUnlock let an improvement of the annotations of the chicken genome adding InterPro annotations to the data set file. IPA provides two powerful tools to understand the pathway analysis results: the networks and canonical pathways that showed several pathways related to an adaptative immune response.