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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

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Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis.

Ángeles Jiménez-Marín¹, Melania Collado-Romero¹, María Ramirez-Boo¹

¹Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Campus de Rabanales, Edificio C-5, 14071 Córdoba, Spain.

BMC Proceedings

|July 21, 2009

Summary

Pathway analysis tools ArrayUnlock and Ingenuity Pathways Analysis (IPA) identified altered biological functions in chicken Eimeria maxima infection. Both tools revealed immune system pathways, aiding host reaction studies.

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Area of Science:

* Poultry immunology
* Bioinformatics
* Genomics

Background:

* Post-microarray analysis is crucial for identifying biological processes.
* Two pathway analysis tools, ArrayUnlock and Ingenuity Pathways Analysis (IPA), are compared.
* Study uses chicken infection data to investigate host reactions to Eimeria challenge.

Purpose of the Study:

* To evaluate ArrayUnlock and IPA for post-microarray analysis of chicken infection data.
* To identify biological functions altered during Eimeria maxima infection.
* To compare the utility of ArrayUnlock and IPA in interpreting complex biological data.

Main Methods:

* Microarray data from chicken Eimeria maxima infection.
* Application of ArrayUnlock for functional enrichment analysis.
* Application of Ingenuity Pathways Analysis (IPA) for pathway and network analysis.

Main Results:

* Both ArrayUnlock and IPA identified altered biological and molecular functions, including immune system pathways.
* Differential biological functions were observed in homologous and heterologous secondary infections.
* The timing of homologous secondary infections impacted several biological functions.

Conclusions:

* ArrayUnlock and IPA yielded similar conclusions regarding functional differences in chicken infection models.
* ArrayUnlock enhanced chicken genome annotations with InterPro data.
* IPA's networks and canonical pathways highlighted adaptive immune response pathways.