Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data

Abstract Biological processes, especially developmental processes, are often dynamic. Previous BodyMap projects for human and mouse have provided researchers with portals to tissue-specific gene expression, but these efforts have not included dynamic gene expression patterns. Over the past few years...

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Published in:Briefings in bioinformatics 2018-11, Vol.19 (6), p.1302-1309
Main Authors: Cui, Ya, Chen, Xiaowei, Niu, Yiwei, Wang, Dongpeng, Luo, Huaxia, Fan, Zhen, Wang, Dan, Wu, Wei, Teng, Xueyi, He, Shunmin, Luo, Jianjun, Chen, Runsheng
Format: Article
Language:English
Subjects:
Biological activity
Browsing
Data bases
Databases, Factual
Developmental biology
Exploration
Gene expression
Gene Expression Profiling
Gene sequencing
Genes
Internet
Knowledge bases (artificial intelligence)
Molecular modelling
Proteins
Ribonucleic acid
RNA
Sequence Analysis, RNA - methods
Time series
Tissues
User-Computer Interface
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Summary:Abstract Biological processes, especially developmental processes, are often dynamic. Previous BodyMap projects for human and mouse have provided researchers with portals to tissue-specific gene expression, but these efforts have not included dynamic gene expression patterns. Over the past few years, substantial progress in our understanding of the molecular mechanisms of protein-coding and long noncoding RNA (lncRNA) genes in development processes has been achieved through numerous time series RNA sequencing (RNA-seq) studies. However, none of the existing databases focuses on these time series data, thus rendering the exploration of dynamic gene expression patterns inconvenient. Here, we present Dynamic BodyMap (Dynamic-BM), a database for temporal gene expression profiles, obtained from 2203 time series of RNA-seq samples, covering >25 tissues from five species. Dynamic-BM has a user-friendly Web interface designed for browsing and searching the dynamic expression pattern of genes from different sources. It is an open resource for efficient data exploration, providing dynamic expression profiles of both protein-coding genes and lncRNAs to facilitate the generation of new hypotheses in developmental biology research. Additionally, Dynamic-BM includes a literature-based knowledgebase for lncRNAs associated with tissue development and a list of manually selected lncRNA candidates that may be involved in tissue development. Dynamic-BM is available at http://bioinfo.ibp.ac.cn/Dynamic-BM.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbx059