Number of circRNAs in organs/seedling and whole plant:
Export filtered results to excel
About At-C-RNA
Arabidopsis thaliana circular RNA database (At-C-RNA) was designed to accommodate circular RNAs identified in Arabidopsis thaliana across different studies. The database encompasses datasets from our recent studies (1,2) as well as those previously available in the public domain. Thanks to the extensive reanalysis and curation of publicly available data, At-C-RNA delivers results in a unified format, making circRNA comparisons between organs, variants, and studies feasible.
In the table, you can see all circRNAs stored in our database. You can find circRNAs that you are interested in by sorting data by any column, setting filters, and selecting/deleting records. Below you can read about each function and column in detail.
Sorting
Clicking on the title of a specific column will sort a table according to this column.
Searching
Each column has a window where you can type criteria to search (possible checkbox states: - true, - false, - indeterminate). When done, click the loop icon to apply the filters.
Deleting
You can delete circRNAs by selecting them in the checkboxes and clicking the trash button. Notice! If you select one circRNA and then select the next one with the shift key you will check all circRNAs between them.
Extended information about specific circRNA
After clicking on each record, you can see a table containing detailed information about a selected circRNA, including the plant organs and lines where it was identified as well as information on the individual scores, circRNA reproducibility and confirmation by RNAse R. See visualization below.
Column description
Column name
Column description
By clicking on the loop icon, you can apply selected filters.
By clicking on the trash icon, you can delete selected records (you can select multiple rows by selecting the first one and the last one with the shift button).
By clicking on the filter icon, you can go back to the default filters.
circRNA ID
CircRNA identifier. Clicking the identification will take you to the EnsemblPlants genomic browser, where you can see the circRNA location in the genome.
Chr
The number of the chromosome where the circRNA is encoded.
Start
Position of the nucleotide where the circRNA starts.
End
Position of the nucleotide where the circRNA ends.
gene ID
Gene identifier. Clicking the gene ID will take you to the NCBI page, where you can see detailed information about a selected gene.
Average score
An average normalized At-C-RNA score computed for the circRNA.
Type
Type of circRNA.
circRNA strand
A strand on which a circRNA is encoded.
Gene strand
A strand on which the gene producing circRNA is located.
Length
Genomic length of a circRNA.
RNaseR confirmed
Information on whether a circRNA was confirmed in the experiment with RNase R treatment (RNase R digests linear RNA).
Reproducibility
Information on whether circRNA is produced in a reproducible manner (identified in >4 biological replicates).
Plant
Plant in which a circRNA was identified.
Organ
The plant organ in which a circRNA was identified.
Line
Line of the plant.
Study
Link to the study where a circRNA was identified.
Statistics
On the first chart of the statistics section, you can see the number of circRNAs produced by a specific organ/seedling. For example, in the beginning, there are 228 common circRNAs produced by flowers, leaves, roots and seedlings. On the second chart, you can see the number of circRNAs from specific chromosomes. For example, in the beginning, there are 181 circRNAs from chromosome 1. On the third chart, you can see the number of genes with a specific number of circular RNA isoforms. For example, in the beginning, the table contains 11 genes with only one circular RNA isoform. On the fourth chart, circRNAs with At-C-RNA scores in the specified range can be seen. For example, in the beginning, there are 397 circRNAs in the table with an At-C-RNA score in the range (0-5]. Notice that when you click on the score range or amount of isoforms of interest on the chart, the table will show you information for only the specified circRNAs. Additionally, charts are updated corresponding to searches and deletions from the table. See the examples below.
Export results to Excel
This section allows you to export the filtered table as an Excel file. Additionally, there is a possibility to define columns in the table to make a pivot table and plot. The bar chart on the right shows an example of a visualization that you can make using a pivot table (Type and RNase R confirmed columns). If all pivots are already defined, or you do not want a pivot table just click "Excel Report" to download your results. To download all the data from the database click, “All data excel report” (regardless of filtering).
It is important to maintain consistency and uniformity in the database, so we decided to include only the data analyzed in a manner consistent with ours. If you wish to update our database with your own data, please send the SRA ID where the raw reads are stored to the email below. In addition, we scan the public domain for new datasets to keep our database up-to-date.
Contact:
Z. Noskowskiego str. 12/14
61-704 Poznań
email: kkozlowska@ibch.poznan.pl
