ChIPBase: decoding the transcriptional regulation of microRNA and lncRNA genes from ChIP-Seq data

microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) and 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 (, a novel database that we have developed to facilitate the comprehensive annotation and discovery of transcription factor binding maps and transcriptional regulatory relationships of miRNAs and lncRNAs from ChIP-Seq data.

chipBase workflow

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, we constructed TF->miRNA->mRNAs regulatory networks by integrating CLIP-Seq data and ChIP-Seq data. In addition, we constructed expression profiles of human lncRNAs and mRNAs from RNA-Seq data from 22 normal tissues.

The ChIPBase is available at

Yang JH, Li JH, Jiang S, Zhou H and Qu LH.
ChIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.
Nucleic Acids Res. 2013, First published online: November 17, 2012.

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