title: ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.
abstract: Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) represent two classes of important non-coding RNAs in eukaryotes. Although these non-coding RNAs have been implicated in organismal development and in various human diseases, surprisingly little is known about their transcriptional regulation. Recent advances in chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-Seq) have provided methods of detecting transcription factor binding sites (TFBSs) with unprecedented sensitivity. In this study, we describe ChIPBase (http://deepbase.sysu.edu.cn/chipbase/), a novel database that we have developed to facilitate the comprehensive annotation and discovery of transcription factor binding maps and transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. The current release of ChIPBase includes high-throughput sequencing data that were generated by 543 ChIP-Seq experiments in diverse tissues and cell lines from six organisms. By analysing millions of TFBSs, we identified tens of thousands of TF-lncRNA and TF-miRNA regulatory relationships. Furthermore, two web-based servers were developed to annotate and discover transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. In addition, we developed two genome browsers, deepView and genomeView, to provide integrated views of multidimensional data. Moreover, our web implementation supports diverse query types and the exploration of TFs, lncRNAs, miRNAs, gene ontologies and pathways.
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Yang
authors.forename: Jun-Hao
authors.initials: JH
authors.lastname: Li
authors.forename: Shan
authors.initials: S
authors.lastname: Jiang
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.forename: Liang-Hu
authors.initials: LH
authors.lastname: Qu
mesh_terms: D000818:Animals; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D030541:Databases, Genetic; D004285:Dogs; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D014157:Transcription Factors