Sidra Medicine, Al Gharrafa Street Ar-Rayyan, Doha, Qatar.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz066.
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.
过敏的患病率在发达国家已达到人口的 20%左右，学龄儿童对一种或多种过敏原的致敏率接近 50%。然而，特应性过敏易感性/发展和环境因素的复杂性使得鉴定基因生物标志物具有挑战性。公开可获得的转录组数据量为跨研究的机制发现和复杂疾病特征的验证提供了前所未有的机会。然而，这需要结构化的方法和可视化工具来解释结果。在这里，我们展示了一个经过精心整理的与免疫球蛋白 E 介导的特应性疾病相关的转录组数据集集合（从过敏到原发性免疫缺陷）。来自基因表达综合数据库的 33 个数据集，包含 1860 个转录组谱，可在基因表达浏览器（GXB）上使用，这是一个在线和开源的网络应用程序，允许查询、可视化和注释元数据。描述了集合的主题组成、疾病类别、样本数量和平台。排名基因列表和样本分组用于促进数据可视化/解释，并可通过 GXB 在线获得（http://ige.gxbsidra.org/dm3/geneBrowser/list）。使用相关出版物进行数据集验证表明，GXB 中的基因表达趋势和倍数变化具有良好的一致性。
