ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data
By Jianhua Yang, Junhao Li, Shan Jiang, Hui Zhou, Liang-Hu Qu. Nucleic Acids Res., 2012
320 citations recorded by the source corpus.
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.
Subfields: Cancer Research, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/c8c47f54556fecfc55d4c4c4f0b8006c149bfef4
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Citations in the corpus
- METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m6A Modification (2017, methodology): “ChIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-seq data.”
- Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers (2015, background): “ChIPBase (12) is focused on the transcriptional regulation of miRNAs and lncRNAs.”
- Revealing protein–lncRNA interaction (2015, unknown): “The ChIPBase database [126] is one example of integrative resource in which regulatory mechanisms formed between lncRNAs, microRNAs and tran-”
- HMDD v2.0: a database for experimentally supported human microRNA and disease associations (2013, background): “These databases have shown their great helps in providing valuable miRNA-related information such as sequences (3), experimentally supported miRNA targets (8–10), mutations (11–13), experimentally supported miRNA transcription factors (14,15), miRNA–drug interactions (16,17) and miRNA-associated dis”
- TANRIC: An interactive open platform to explore the function of lncRNAs in cancer (2015, unknown): “Compared with other available lncRNA-focused bioinformatics resources (11,25-34), TANRIC has several unique features (Table 2): (i) It provides extensive, intuitive and interactive analyses on lncRNAs of interest for”
- lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs (2014, background): “0 (10), chromatin state of lncRNAs can be investigated at ChIPBase (11) and the ability for lncRNAs to act as competitive endogenous RNA (ceRNA) can be investigated at lnCeDB (12).”
- ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data (2016, methodology): “0) (14), the advances and improvements of ChIPBase v2.”