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TRCirc provides a comprehensive data source for integrating current transcription factors binding sites and circRNA annotations. The current release of TRCirc contains approximately 92375 human circRNAs and 690 ChIP-seq data sets across 91 human cell lines for 161 unique regulatory factors.Moreover, TRCirc provides other information of circRNAs, such as enhancer, methylation level, H3K27ac signal and expression. TF2LncRNA is an efficient and easy-to-use web-based tool.

1.TRCirc collected circRNA annotations and ChIP-seq and RNA-seq data sets from circBase and ENCODE, respectively.

2.TRCirc defined a region from 2kb upstream to 1kb downstream of the transcription start site of each circRNA as its regulatory region based on previous research. Meanwhile, we defined other regulatory regions, such as -10kb/1kb,-20kb/1kb, -30kb/2kb in the database.

3.TF-CircRNA regulatory relationships: Mapped transcription factors binding sites to regulatory region of circRNA.

4.TRCirc also include other information of circRNAs:super-enhancer, methylation, H3K27ac signal, junction reads and RPKM.

5.TRCirc provided visualization of network that about TFs-circRNA regulatory relationship in each cell lines.

6.TRCirc also provided visualization about expression of circRNA.

7.TRCirc JBrowse was developed to visualize transcriptional regulation information of circRNA.

Advanced Search

In this search entrance, accurate search is supported. User can specify the detailed information about circRNAs such as species, cell type, cell, regulation regions and circRNA name etc.

Class: Cell type

Cell: Cell lines

CircRNA: CircRNA ID

Regulation_region:Promoter of circRNAs (-2Kb/1Kb, -10Kb/1Kb, -20Kb/1Kb and -30Kb/2Kb of a TSS)

TF: Number of transcription factor which regulate that circRNA

SE/TE: Number of enhancer(super-enhancer and typical enhancer) which regulate that circRNA

Methylation: Mean of methylation level of that circRNA

H3K27ac: H3K27ac signal in regulatory region (±1Kb of a TSS) of that circRNA

Junction_read: Quantification of circRNA expression by junction reads

RPKM-circRNA: Quantification of circRNA expression by reads of body region

RPKM-gene: Quantification of host gene expression by reads of body region


Search and Browse TF-circRNAs Regulatory Relationship by TF

Cell_lines_name: All cell lines for this transcription factor

Official_symbol: Official name of Transcription factor

antibody: Corresponding antibody for transcription factor in each Chip-seq experiment

TF_peak: Transcription factor binding site of regulatory region of circRNA

CircRNA_name: CircRNA ID

CircRNA_TSS: Transcription start sites of circRNA

Strand: +; -

Distance_peak2TSS: Distance between peak center and TSS of circRNA.


Search and Browse TF-circRNAs Regulatory Relationship by Cell Lines

Cell_lines_name: All cell lines for this transcription factor

Official_symbol: Official name of Transcription factor

antibody: Corresponding antibody for transcription factor in each Chip-seq experiment

TF_peak: Transcription factor binding site of regulatory region of circRNA.

CircRNA_name: CircRNA ID

CircRNA_TSS: Transcription start sites of circRNA

Strand: +; -

Distance_peak2TSS: Distance between peak center and TSS of circRNA


Search and Browse Methylation State of circRNAs

Score: Scores associated with each site are beta values multiplied by 1000


Search and Browse enhancer which association with circRNAs

SE/TE: Super-enhancer or typical enhancer which regulate that circRNA

isSuper: Whether is super-enhancer


Visualization

In this search entrance, User can specify the information about circRNAs such as species, cell, regulation regions and circRNA name etc. User can obtain visualization of TF-circRNA network and expression of that circRNA.To arise user experience, TRCirc providing visualization of one circRNAs at a time. Moreover, JBrowse was used to visualize transcriptional regulation information of circRNA.


Data Visualization

#TFs that in table correspond with TFs in network of bottom


JBrowse

JBrowse was used to visualize transcriptional regulation information of circRNA.Including the enhancer, TFBS, methylation and common SNP.

You can download TF-CircRNA regulatory relationships of four classes regulatory region by transcription factor and cell lines. And you can download TF-CircRNA pairs of four classes regulatory region, which does not distinguish transcription factor and cell line. Furthermore, user can download comprehensive information of circRNA and expression (standardization by H3K27ac signal, junction reads and body reads) of circNRAs.


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