PD-NGSAtlas: A reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders

Zheng Zhao, Yongsheng Li, Hong Chen, Jianping Lu, Peter M. Thompson, Juan Chen, Zishan Wang, Juan Xu, Chun Xu, Xia Li

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Background: Psychiatric disorders such as schizophrenia (SZ) and bipolar disorder (BP) are projected to lead the global disease burden within the next decade. Several lines of evidence suggest that epigenetic- or genetic-mediated dysfunction is frequently present in these disorders. To date, the inheritance patterns have been complicated by the problem of integrating epigenomic and transcriptomic factors that have yet to be elucidated. Therefore, there is a need to build a comprehensive database for storing epigenomic and transcriptomic data relating to psychiatric disorders. Description: We have developed the PD-NGSAtlas, which focuses on the efficient storage of epigenomic and transcriptomic data based on next-generation sequencing and on the quantitative analyses of epigenetic and transcriptional alterations involved in psychiatric disorders. The current release of the PD-NGSAtlas contains 43 DNA methylation profiles and 37 transcription profiles detected by MeDIP-Seq and RNA-Seq, respectively, in two distinct brain regions and peripheral blood of SZ, BP and non-psychiatric controls. In addition to these data that were generated in-house, we have included, and will continue to include, published DNA methylation and gene expression data from other research groups, with a focus on psychiatric disorders. A flexible query engine has been developed for the acquisition of methylation profiles and transcription profiles for special genes or genomic regions of interest of the selected samples. Furthermore, the PD-NGSAtlas offers online tools for identifying aberrantly methylated and expressed events involved in psychiatric disorders. A genome browser has been developed to provide integrative and detailed views of multidimensional data in a given genomic context, which can help researchers understand molecular mechanisms from epigenetic and transcriptional perspectives. Moreover, users can download the methylation and transcription data for further analyses. Conclusions: The PD-NGSAtlas aims to provide storage of epigenomic and transcriptomic data as well as quantitative analyses of epigenetic and transcriptional alterations involved in psychiatric disorders. The PD-NGSAtlas will be a valuable data resource and will enable researchers to investigate the pathophysiology and aetiology of disease in detail.

Original languageEnglish (US)
Article number71
JournalBMC Medical Genomics
Volume7
Issue number1
DOIs
StatePublished - 2014

Keywords

  • Bipolar disorder
  • Blood
  • Brain
  • Epigenomic and transcriptomic data
  • Next-generation sequencing
  • Schizophrenia

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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