Welcome to TRCirc

High-throughput genomic technologies like ChIP-seq and RNA-seq become more and more mature and inexpensive. A large number of circular RNAs (circRNAs) from back-spliced exons have been identified in various cell lines and across different species. However, transcriptional regulatory function of abundant circRNAs is unclear, so building a database of transcriptional regulatory information of circRNA is necessary. Here, based on ChIP-seq peaks of transcription factors binding sites (TFBSs) of each cell lines from ENCODE and all annotated human circRNAs from circBase, we developed a data source titled “TRCirc”, where enriched regions of TFBSs (peaks) from ChIP-seq experiments crossed with the regulatory region of circRNAs by their genomic coordinates, if a TFBS is located within the regulatory region of a certain circRNA, they form a TF and circRNA regulatory relationship (TF-circRNA). Moreover, TRCirc also provided other correlation information, such as methylation level, H3K27ac signals, super-enhancers and expression of circRNAs. The current release of TRCirc incorporates 92375 circRNAs and 161 TFs in more than 100 cell types, involving the 690 uniform TFBS, 36 H3K27ac, 54 RNA-seq and 61 450k data sets. Users can search and browse TFBSs of circRNAs and other correlation information for particular TFs, cell lines or circRNAs of interest. Our tool also capacitates researchers to easily download TF-circRNA interactions for four classes regulatory region and other correlation information. TRCirc is contributing to discovering transcription regulation mechanism of circRNAs. The Google Chrome and Mozilla Firefox with 1440*900 are preferred to achieve the best display effect.

Overview of data in TRCirc

Topological of TF-circRNAs network

  • Regulatory region:-2K/+1K
  • x axis:Degree of circRNAs
  • y axis:Number of circRNAs(10^3)

Number of TF-circRNA pairs in each cell line

  • Regulatory region:-2K/+1K
  • x axis:cell line
  • y axis:Number of TF-circRNA pairs(10^3)

Histogram of TF regulation circRNA

  • Regulatory region:-2K/+1K
  • x axis:TF
  • y axis:Number of circRNAs(10^3)

Publication

Zhidong Tang, Xuecang Li, Jianmei Zhao, Fengcui Qian, Chenchen Feng, Yanyu Li, Jian Zhang, Yong Jiang, Yongsan Yang, Qiuyu Wang, Chunquan Li; TRCirc: a resource for transcriptional regulation information of circRNAs, Briefings in Bioinformatics, bby083, https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bby083/5089935.

Sister Projects

SEanalysis: A web tool for super-enhancer associated regulatory analysis

SEdb: The comprehensive human Super-Enhancer database

KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors

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