PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders

BMC Medical Genomics

Xia Li³  Chun Xu¹  Juan Xu³  Zishan Wang³  Juan Chen³  Peter M Thompson²  Jianping Lu³  Hong Chen³  Yongsheng Li³  Zheng Zhao³ 

[1] Department of Pediatrics, Paul L. Foster School of Medicine, Texas Tech University Health Science Center, El Paso, TX, USA;Southwest Brain Bank, Department of Psychiatry, UTHSCSA, San Antonio, TX, USA;College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China

关键词: Blood;    Brain;    Epigenomic and transcriptomic data;    Next-generation sequencing;    Bipolar disorder;    Schizophrenia;   

Others  :  1090039
DOI  :  10.1186/s12920-014-0071-z

 received in 2014-09-22, accepted in 2014-12-11,  发布年份 2014

【 摘 要 】

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. The database is available at http://bioinfo.hrbmu.edu.cn/pd_ngsatlas/ webcite.

【 授权许可】

   
2014 Zhao et al.; licensee BioMed Central.

【 图 表 】

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