Contents

• 1. Searching
• 2. Results
• 3. Information of circRNAs
• 4. UCSC Genome Browser trackhub
• 5. Information of miRNAs related to circRNA
• 6. Discovery for miRNA-circRNA interactome
• 7. Downloading data
• 8. About

1. Searching

There are three manners to search in circBank database: simple quick search, search by circRNA information and search by miRNA information

Simple quick search

Users can search circRNA directly in the Home page of circBank database. Users can search relative circRNAs by querying the database by circBank ID number (e.g.hsa_circHIPK3_001), circBase ID number (e.g.hsa_circ0021592), gene symbol (e.g.HIPK3) and refseq transcript ID (e.g.NM_005734). Searching results will show in a new page.

Search by circRNA information

Users can also search circRNA under “circRNA” page. In this page, users can query the database by single item or multiple item combinations, including Gene name (gene symbol), circBank ID number, circBase ID number. Users also can filter related information by checking the circRNA conservation, circRNA m6A and setting the Protein coding potential.

Search by miRNA information

Users can also search circRNA under “miRNA” page. The “miRNA” page was designed to convenient for users to search for miRNA-related circRNAs of interest. In the “miRNA” page, users can query the database by single item or multiple item combinations, including miRNA ID (e.g. has-miR-30a-3p), circBank ID number, circBase ID number. Users also can filter related information by checking the circRNA conservation, circRNA modification and setting the Protein coding potential.

2. Results

Results for circRNA searching

Results for quick research and circRNA research will be listed in a new page, sorted by the circBank ID number. If searching results were more than 10 records, result default is divided into multiple pages, no more than 10 records per page. Users can change the high listed number of records by select the showing set under the list. Users can also toggle results display style by click the “” button, results will change to message digest format. Users can also select the information shown in the results by checking relative options by click the “” button.

To get more details about specific circRNA, users can click the circBank ID number, information of selected circRNA will be shown in a new page. Users also can click the miRNA site in related row or module, miRNAs related to selected circRNA will be shown in a new page.

Results for miRNA searching

Results for miRNA research will be listed. If searching results were more than 10 records, result default is divided into multiple pages, no more than 10 records per page. Users can change the high listed number of records by select the showing set under the list. Users can also toggle results display style by click the “” button, results will change to message digest format. Users can also select the information shown in the results by checking relative options by click the “” button.

3. Information of circRNAs

There is a whole page for each selected circRNA. In this page, information about circRNA were divided into multiple sections to show different information.

Basic information: the circBank ID, circBase ID, genomic position (hg19) circRNA length, host gene symbol, best matched transcript refseq ID and annotation.

RNA sequence: the whole sequence of certain circRNA. Users can direct copy the sequence.

Conserved mm9 circRNA: the sequence of conserved circRNA in mouse (mm9). Users can direct copy the sequence.

Coding potential assessment: CPAT was used to calculate the coding probability based on the sequence of the circRNA. The logistic regression model based on four features including ORF size, ORF coverage, Fickett TESTCODE and Hexamer usage bias were used to predict coding potential of the circRNA. Fickett_score is the statistic that measures the computational bias between coding and non-coding sequences based on a periodicity of three (every three nucleotides encode one amino acid). Hexamer_score is a log-likelihood ratio to measure differential hexamer usage between coding and noncoding sequences.

IRES elements: IRESfinder was used for the prediction of the IRES elements of certain circRNA.

Mutation: relative mutation information according to COSMIC database.

RNA modification: reported post transcription modification for certain circRNA.

4. UCSC Genome Browser trackhub

CircBank provides a trackhub to directly display the annotations in the UCSC Genome Browser. Click here to load the tracks in the UCSC Genome Browser.

5. Information of miRNAs related to circRNA

Users can get circRNA related miRNAs by two methods: search from “circRNA” channel to get the miRNAs that were predicted to bind to certain circRNAs by clicking the “miRNA” button in the same row of certain in the circRNA searching result list. The other method is to search in the “miRNA” channel to get predicted binding circRNAs to certain miRNA, in this manner, users can get all circRNAs that predicted to bind to certain miRNA or specific circRNA (add the information about specific circRNA in the “miRNA” channel when searching) .

Results of miRNA related to circRNA are listed in a new page. If searching results were more than 10 records, result default is divided into multiple pages, no more than 10 records per page. Users can change the high listed number of records by select the showing set under the list. Users can also toggle results display style by click the “” button, results will change to message digest format. Users can also select the information shown in the results by checking relative options by click the “” button.

Information of miRNA related to circRNA including the circBank ID, circBase ID, circRNA length, miRNA ID (miR_ID), miRanda binding site positions (predicted by miRanda), targetscan binding site positions (predicted by targetscan).

6. Discovery for miRNA-circRNA interactome

Users can analysis the interactome of miRNAs and circRNAs by a variety of effective search tools in circBank database.

Discovery group of miRNAs binding to certain circRNA: Users can get a group of miRNAs that predicted binding to certain circRNA. Combining several information about certain circRNA, including mutation site of circRNA, modification of circRNA as well as conserved mm9 circRNA, users can analyze in-depth for the miRNA binding site that maybe influenced by point mutation, modification and the evolutionary conservation.

Discovery group of circRNAs that bind to same miRNA: Users can get a group of circRNAs that predicted to bind the same miRNA by searching under “miRNA” channel. In this way, users can get panoramic information about whole circRNA group inner human genome that related to the certain miRNA. Combining with the deep sequence data, users can get a circRNA interactome network for certain miRNA.

7. Downloading Data

In circBank database, users can download data of txt formation through download channel. Including circRNA annotation, circRNA sequence, circRNA conservation, miRNA-circRNA ineractions, circRNA Modification, circRNA protein coding potential.

8. About

CircBank database is developed and maintained by Guangzhou Geneseed Biotech. Co., Ltd. in China.