A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.

Susie S Y Huang,Damien Chaussabel,Mohammed Toufiq,Fatima Al Ali,Sabri Boughorbel,Mathieu Garand

doi:10.1093/database/baz066

Susie S Y Huang, Damien Chaussabel + Show 4 more

Open Access

https://doi.org/10.1093/database/baz066

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Abstract

Prevalence of allergies has reached ~20% of population in developed countries and sensitization rate to one or more allergens among school age children are approaching 50%. However, the combination of the complexity of atopic allergy susceptibility/development and environmental factors has made identification of gene biomarkers challenging. The amount of publicly accessible transcriptomic data presents an unprecedented opportunity for mechanistic discoveries and validation of complex disease signatures across studies. However, this necessitates structured methodologies and visual tools for the interpretation of results. Here, we present a curated collection of transcriptomic datasets relevant to immunoglobin E-mediated atopic diseases (ranging from allergies to primary immunodeficiencies). Thirty-three datasets from the Gene Expression Omnibus, encompassing 1860 transcriptome profiles, were made available on the Gene Expression Browser (GXB), an online and open-source web application that allows for the query, visualization and annotation of metadata. The thematic compositions, disease categories, sample number and platforms of the collection are described. Ranked gene lists and sample grouping are used to facilitate data visualization/interpretation and are available online via GXB (http://ige.gxbsidra.org/dm3/geneBrowser/list). Dataset validation using associated publications showed good concordance in GXB gene expression trend and fold-change.

Highlights

Allergic disease is highly prevalent and currently reaches ∼20% of the populations in developed nations and with sensitization rate to one or more allergens among school age children approaching 40%–50% [1]
The generation of allergic responses is well understood, the early sensitization steps and factors contributing to the development of immunoglobin E (IgE)-mediated diseases remain unclear
Atopy is defined by the American Academy of Allergy, Asthma and Immunology as the genetic tendency to develop allergic diseases such as allergic rhinitis, asthma and atopic dermatitis and is typically associated with heightened immune responses to common allergens, especially inhaled allergens and food allergens

Summary

Introduction

Allergic disease is highly prevalent and currently reaches ∼20% of the populations in developed nations and with sensitization rate to one or more allergens among school age children approaching 40%–50% [1]. The generation of allergic responses is well understood, the early sensitization steps and factors contributing to the development of immunoglobin E (IgE)-mediated diseases remain unclear. IgE is the major mediator of atopic response in humans. Atopy is defined by the American Academy of Allergy, Asthma and Immunology as the genetic tendency to develop allergic diseases such as allergic rhinitis, asthma and atopic dermatitis (eczema) and is typically associated with heightened immune responses to common allergens, especially inhaled allergens and food allergens. Not all encounters with a potential allergen will lead to sensitization. Not all sensitizations will result in a symptomatic allergic response even in atopic individuals

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