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A curated transcriptome dataset collection to investigate inborn errors of immunity

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submitted on 2024-07-07, 11:57 and posted on 2024-07-07, 11:57 authored by Salim Bougarn, Sabri Boughorbel, Damien Chaussabel, Nico Marr

Primary immunodeficiencies (PIDs) are a heterogeneous group of inherited disorders, frequently caused by loss-of-function and less commonly by gain-of-function mutations, which can result in susceptibility to a broad or a very narrow range of infections but also in inflammatory, allergic or malignant diseases. Owing to the wide range in clinical manifestations and variability in penetrance and expressivity, there is an urgent need to better understand the underlying molecular, cellular and immunological phenotypes in PID patients in order to improve clinical diagnosis and management. Here we have compiled a manually curated collection of public transcriptome datasets mainly obtained from human whole blood, peripheral blood mononuclear cells (PBMCs) or fibroblasts of patients with PIDs and of control subjects for subsequent meta-analysis, query and interpretation. A total of eighteen (18) datasets derived from studies of PID patients were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) database and loaded in GXB, a custom web application designed for interactive query and visualization of integrated large-scale data. The dataset collection includes samples from well characterized PID patients that were stimulated ex vivo under a variety of conditions to assess the molecular consequences of the underlying, naturally occurring gene defects on a genome-wide scale. Multiple sample groupings and rank lists were generated to facilitate comparisons of the transcriptional responses between different PID patients and control subjects. The GXB tool enables browsing of a single transcript across studies, thereby providing new perspectives on the role of a given molecule across biological systems and PID patients. This dataset collection is available at http://pid.gxbsidra.org/dm3/geneBrowser/list.

Other Information

Published in: F1000Research
License: http://creativecommons.org/licenses/by/4.0/
See article on publisher's website: https://dx.doi.org/10.12688/f1000research.18048.2

Funding

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

History

Language

  • English

Publisher

F1000 Research

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

Bougarn, S., Boughorbel, S., Chaussabel, D., & Marr, N. (2019). A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. F1000Research, 8, 284. https://doi.org/10.12688/f1000research.18533.1. SIDRA : GBX : Gene Expression Browser. http://vri1.gxbsidra.org/dm3/geneBrowser/list Bougarn, S., Boughorbel, S., Chaussabel, D., & Marr, N. (2019). A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. F1000Research, 8, 284. https://doi.org/10.12688/f1000research.18533.1. National Institutes of Health : National Center for Biotechnology Information : Genes & Expressions : Gene Expression Omnibus (GEO) Datasets : Accession number GSE92466. https://www.ncbi.nlm.nih.gov/gds/?term=GSE92466

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