Biological pathway analysis by ArrayUnlock and Ingenuity Pathway AnalysisReport as inadecuate




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BMC Proceedings

, 3:S6

First Online: 16 July 2009DOI: 10.1186-1753-6561-3-S4-S6

Cite this article as: Jiménez-Marín, Á., Collado-Romero, M., Ramirez-Boo, M. et al. BMC Proc 2009 3Suppl 4: S6. doi:10.1186-1753-6561-3-S4-S6

Abstract

BackgroundOnce 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.

ResultsAnalysis 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.

ConclusionFunctional 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.

Electronic supplementary materialThe online version of this article doi:10.1186-1753-6561-3-S4-S6 contains supplementary material, which is available to authorized users.

Ángeles Jiménez-Marín, Melania Collado-Romero contributed equally to this work.

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Author: Ángeles Jiménez-Marín - Melania Collado-Romero - María Ramirez-Boo - Cristina Arce - Juan J Garrido

Source: https://link.springer.com/







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