College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
BGI-Shenzhen, Shenzhen, 518083, People's Republic of China.
BMC Med Genomics. 2021 Nov 4;14(1):260. doi: 10.1186/s12920-021-01110-x.
Birth defects pose a major challenge to infant health. Thus far, however, the causes of most birth defects remain cryptic. Over the past few decades, considerable effort has been expended on disclosing the underlying mechanisms related to birth defects, yielding myriad treatises and data. To meet the increasing requirements for data resources, we developed a freely accessible birth defect multi-omics database (BDdb, http://t21omics.cngb.org ) consisting of multi-omics data and potential disease biomarkers.
In total, omics datasets from 136 Gene Expression Omnibus (GEO) Series records, including 5245 samples, as well as 869 biomarkers of 22 birth defects in six different species, were integrated into the BDdb. The database provides a user-friendly interface for searching, browsing, and downloading data of interest. The BDdb also enables users to explore the correlations among different sequencing methods, such as chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) from different studies, to obtain the information on gene expression patterns from diverse aspects.
To the best of our knowledge, the BDdb is the first comprehensive database associated with birth defects, which should benefit the diagnosis and prevention of birth defects.
出生缺陷对婴儿健康构成重大挑战。然而，迄今为止，大多数出生缺陷的原因仍不清楚。在过去的几十年中，人们已经投入了大量的努力来揭示与出生缺陷相关的潜在机制，产生了无数的论文和数据。为了满足对数据资源不断增长的需求，我们开发了一个免费访问的出生缺陷多组学数据库（BDdb，http://t21omics.cngb.org），其中包含多组学数据和潜在的疾病生物标志物。
总共整合了来自 136 个基因表达综合数据库（GEO）系列记录的组学数据集，包括 5245 个样本，以及 6 个不同物种的 22 种出生缺陷的 869 个生物标志物。该数据库提供了一个用户友好的界面，用于搜索、浏览和下载感兴趣的数据。BDdb 还使用户能够探索不同测序方法之间的相关性，例如来自不同研究的染色质免疫沉淀测序（ChIP-Seq）和 RNA 测序（RNA-Seq），从而从多个方面获得基因表达模式的信息。
据我们所知，BDdb 是第一个与出生缺陷相关的综合数据库，它应该有助于出生缺陷的诊断和预防。
