Manual of VirusCircBase
Intructions
Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that are involved in transcriptional and posttranscriptional gene expression regulation. Typical circular RNA molecules comprise canonically spliced exonic sequences and are covalently closed. They have recently been shown to be expressed in microbiology, including virus.
In VirusCircBase, we firstly obtained 56 datasets from NCBI SRA database which searched by the keyword of "virus" and screened by some other keywords such as "rRNA-depleted", "RNase R" and "polyA-RNA depleted" . Then, the circRNAs were identified with three tools : CIRI2, find_circ, circRNA_finder. In total,we detected 46,400 circRNAs in 26 viruses from 15 viral families. The circRNAs and their related information , including location , expression , sources , were provided in the database.
Detail information of an entry
For each entry in VirusCircBase, a list of items have been displayed. The table below describes the detailed meaning of each item.
|
circRNA name |
In our naming system , each circRNA have an unique number in our database, an abbreviation for the corresponding virus and the host infected by virus. Finally,the three parts were connected with '_circ_'. |
|
Viralgenome |
The accession number of the reference genome used in VirusCircBase. |
|
Start |
Start site of the circRNA in reference sequence. |
|
End |
End site of the circRNA in reference sequence. |
|
Strand |
Strand information. |
|
Gene |
The virus genes in which the circRNA is involved . |
|
Junction read counts |
CircRNA junction read counts.( The total number of reads that support the junction of the circRNA. ) |
|
Detection tool |
Bioinformatics tools used to identify circRNA. |
|
Host |
Host of the virus. |
|
Cell/tissue |
Cell or tissue infected by the virus |
|
Virus name |
Name of the virus |
|
Virus taxid |
ID of the virus in NCBI Taxonomy database |
|
Genomic length |
Genomic length of the viral genome |
|
GEO |
NCBI SRA or GEO information corresponding to the dataset. |
|
Sample |
The sample information corresponding to the SRA dataset. |
|
PMID |
The paper in which the circRNA was verified by experiments. |
miRNA
Potential interaction between miRNAs and circRNAs were predicted using TarPmiR. For each circRNA, the miRNAs which may interact with the circRNA were provided . Besides , the interaction probability and interaction region were also provided.
Submit your data
If you would like to submit your data to VirusCircBase, or to suggest implementation of a published circRNA dataset, please contact us by Email : pys2013@hnu.edu.cn
About us
VirusCircBase is developed by the Peng lab
in College of Biology, Hunan University, Changsha, China .
Email: pys2013 AT hnu.edu.cn