Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh 173234, India.
Department of Pulmonary Medicine, Indira Gandhi Medical College, Shimla, Himachal Pradesh 171001, India.
Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay053.
Interstitial lung diseases (ILDs) are a diverse group of ∼200 acute and chronic pulmonary disorders that are characterized by variable amounts of inflammation, fibrosis and architectural distortion with substantial morbidity and mortality. Inaccurate and delayed diagnoses increase the risk, especially in developing countries. Studies have indicated the significant roles of genetic elements in ILDs pathogenesis. Therefore, the first genetic knowledge resource, ILDgenDB, has been developed with an objective to provide ILDs genetic data and their integrated analyses for the better understanding of disease pathogenesis and identification of diagnostics-based biomarkers. This resource contains literature-curated disease candidate genes (DCGs) enriched with various regulatory elements that have been generated using an integrated bioinformatics workflow of databases searches, literature-mining and DCGs-microRNA (miRNAs)-single nucleotide polymorphisms (SNPs) association analyses. To provide statistical significance to disease-gene association, ILD-specificity index and hypergeomatric test scores were also incorporated. Association analyses of miRNAs, SNPs and pathways responsible for the pathogenesis of different sub-classes of ILDs were also incorporated. Manually verified 299 DCGs and their significant associations with 1932 SNPs, 2966 miRNAs and 9170 miR-polymorphisms were also provided. Furthermore, 216 literature-mined and proposed biomarkers were identified. The ILDgenDB resource provides user-friendly browsing and extensive query-based information retrieval systems. Additionally, this resource also facilitates graphical view of predicted DCGs-SNPs/miRNAs and literature associated DCGs-ILDs interactions for each ILD to facilitate efficient data interpretation. Outcomes of analyses suggested the significant involvement of immune system and defense mechanisms in ILDs pathogenesis. This resource may potentially facilitate genetic-based disease monitoring and diagnosis.Database URL: http://14.139.240.55/ildgendb/index.php.
间质性肺疾病（ILDs）是一组约 200 种急性和慢性肺部疾病，其特征是炎症、纤维化和结构扭曲程度不同，发病率和死亡率很高。不准确和延迟的诊断会增加风险，尤其是在发展中国家。研究表明，遗传因素在ILDs 的发病机制中起着重要作用。因此，第一个遗传知识库——ILDgenDB 已经开发出来，旨在为更好地了解疾病发病机制和识别基于诊断的生物标志物提供 ILD 遗传数据及其综合分析。该资源包含文献整理的疾病候选基因（DCGs），这些基因富含各种调控元件，这些元件是通过数据库搜索、文献挖掘和 DCGs- microRNA (miRNAs)-单核苷酸多态性 (SNP) 关联分析的综合生物信息学工作流程生成的。为了提供疾病基因关联的统计学意义，ILD 特异性指数和超几何测试分数也被纳入其中。还对不同亚类 ILD 发病机制的 miRNA、SNP 和途径的关联分析进行了分析。还提供了手动验证的 299 个 DCGs 及其与 1932 个 SNPs、2966 个 miRNAs 和 9170 个 miR-多态性的显著关联。此外，还确定了 216 个文献挖掘和提出的生物标志物。ILDgenDB 资源提供了用户友好的浏览和广泛的基于查询的信息检索系统。此外，该资源还为每个 ILD 提供了预测的 DCGs-SNPs/miRNAs 和与文献相关的 DCGs-ILDs 相互作用的图形视图，以方便有效地解释数据。分析结果表明，免疫系统和防御机制在 ILDs 的发病机制中起着重要作用。该资源可能有助于基于遗传的疾病监测和诊断。数据库网址：http://14.139.240.55/ildgendb/index.php。
