Documents index
The scheme of PsiAtlas workflow: PsiAtlas provides comprehensive information on RNA modifications. For m6A modifications, a total of 693 MeRIP-seq samples were collected from SRA and GSA databases for 20 plant species. In addition, twelve MeRIP-seq datasets of Oryza rufipogon, Oryza sativa ssp. indica, Oryza sativa ssp. japonica were generated in this study. These MeRIP-seq datasets together with other types of RNA modification datasets and additional related datasets were processed through our uniform pipeline. All results were deposited in a MySQL database and displayed in several convenient web modules on PsiAtlas web pages. Furthermore, we developed several convenient tools in PsiAtlas to facilitate users visualizing the data in the database and choose data or samples to perform further analyses.
Web resources have a dependency on internet browsers, and different browsers use different kernels with different approaches. We recommend that users access our database through a Firefox, Chrome or Microsoft Edge browser.
| Browser Name | Supported Version |
|---|---|
| Microsoft Edge | >=112.0.x |
| Firefox | >=116.0.x |
| 360 | >=14.1.x |
| Safari | >=5.1.x |
| Chrome | >=70.0.x |
| Opera | >=101.0.x |
Users can quickly search for the interest gene ID, gene name or PubMed ID from the homepage. You will see the page shown in the screenshot below. Enter the gene name “IPA1" in the Gene/Transcript input box.
The results of the "Search" module in PsiAtlas revealed detailed information about the gene of your interest.
When you click ‘Browse’ from the menu of the homepage,you can choose whether you are interested in NGS or DRS data. If you don't have a specific gene of interest and are particularly looking for cases of pseudouridine modification sites, you can query these in the ‘Browse module’ which displays the NGS datasets or DRS datasets of as query,you can see page as screenshot below.
Browse of other dataset:The below screenshot show a list of the xperimental validation or other methods of the validated NGS dataset.
‘JBrowse’, a comprehensive genomic browser, displays the distribution of pseudouridine sites and their related information with genome coordinates. .
PsiRMVar:to detect potential deleterious variants effects on pseudouridine modification. PsiRMVar allows users to upload their variations files in VCF format to evaluate the effect of pseudouridine modification site.
Query the job status.There are four major steps in the data analysis process: Matrix construction', ‘Variation annotation' and 'job completed'. The page will redirect to the result page when the job status is "job completed".
Retrieving results:Retrieving the results generated by PsiRMVar. In result pages, all the results are showed in high-quality interactive figures and tables. The figures generated by highcharts.js can be downloaded in PNG, JPG, PDF and SVG formats while the table formated by DataTables.js can be download in CSV, Excel and PDF formats.
PsiFinder: A deep learning-based high accuracy Pseudouridine predictor covering Pseudouridine identification in different species.
Retrieving results:Retrieving the results generated by PsiFinder.The table formated by DataTables.js can be download in CSV, Excel and PDF formats.
The PsiAtlas data files can be freely downloaded and used in accordance with the GNU Public License and the license of primary data sources.
The PsiAtlas data files can be freely downloaded and used in accordance with the GNU Public License and the license of primary data sources.
