Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis
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Autor
Jiménez-Marín, Ángeles
Collado-Romero, Melania
Ramírez-Boo, M.
Arce Jiménez, Cristina
Garrido, Juan J.
Editor
BioMed CentralFecha
2009Materia
Pathways analysisExpressed genes
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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