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

journal contribution
submitted on 2024-07-10, 07:01 and posted on 2024-07-10, 07:01 authored by Susie S Y Huang, Fatima Al Ali, Sabri Boughorbel, Mohammed Toufiq, Damien Chaussabel, Mathieu Garand

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.

Other Information

Published in: Database
License: http://creativecommons.org/licenses/by/4.0/
See article on publisher's website: https://dx.doi.org/10.1093/database/baz066

Funding

Qatar National Research Fund (NPRP10-0205-170348), Establishing a Foundation for "Collective Data"-enabled Biomedical Research in Qatar.

History

Language

  • English

Publisher

Oxford University Press

Publication Year

  • 2019

License statement

This Item is licensed under the Creative Commons Attribution 4.0 International License.

Institution affiliated with

  • Sidra Medicine

Related Datasets

SIDRA : GBX : Gene Expression Browser. http://ige.gxbsidra.org/dm3/geneBrowser/list