Introduction
OpenAc4C , the first integrated resource to decode the transcriptome landscape, regulatory mechanisms, and disease pathogenesis of ac4C modification across diverse species spanning vertebrates, mammals, insects, fungi, plants, bacterial, archaea, and viruses. By mining a large array of ac4C epitranscriptome datasets with deep learning-based pipelines, the OpenAc4C offers a comprehensive collection of ac4C-related knowledges include:
1) ac4C acRIP-seq database: The database collection includes 329,086 ac4C enriched regions from validated experiments, covering 8 species, including animals, plants and virus.
2) ac4C High-resolution database: This database contains 104,229 single base sites from two high-resolution profiling techniques and Modomics, covering 14 species including animals, plants, archaea, fungi and HIV.
3) Direct RNA sequencing database: For ac4C sites identified in direct RNA sequencing samples, we collected a total of 76,139 modified cytosines that passed our selection criteria. Each modified cytosine was labeled with an ac4C score (probability), representing putative ONT-based ac4C sites covering 21 species.
4) ac4CDiseaseDB: a database holding the most complete collection of 536,986 ac4C-associated variants that may add or remove an ac4C acetylation site, with 4,766 disease-relevant variants that may shed light on disease mechanisms acting through epitranscriptome layer circuitry.
5) ac4CFinder: a deep learning-based high accuracy ac4C predictor covering ac4C identification in 13 different species.
6) ac4CSNPer: a real-time analysis module to assess the impact of genetic variants on database collection..
User Guide
ac4CDB
1. Select the type of database you want to view (acRIP-seq, base-resolution, direct RNA sequencing) at the top.
2. You can retrieve modification sites specific to certain species, Tissue/Cell Line, Gene region and Technique to obtain unique data and pie charts.
3. You can also filter the results by gene type: Protein Coding, LincRNA, miRNA, snoRNA, etc. Additionally, you can filter by a specific position.
4. Click the 'ID' to view the detailed description of individual site. RNA binding protein information, miRNA target, splicing will be shown if available.
5. View specific ac4C site in genome browser by clicking the 'JBrowser' button.
ac4CDiseaseDB
1. Choose Species under 'ac4CDiseaseDB' category.
2. You can retrieve mutation sites specific to certain species, ac4C Status, Confidence Level and Association Level to obtain unique data, corresponding pie charts.
ac4CFinder
1. Click 'ac4CFinder' under 'Tool' category.
2. Select the appropriate Genome Assemble, Instance Length, Threshold.
3. Input query sequences (FASTA) in the box or upload a FASTA file, designate parameters (default values are acceptable), and then click 'submit'. Results will be displayed when the job is completed (may take several seconds).Note: please allow pop-up for Safari browser.
ac4CSNPer
1. Click 'ac4CSNPer' under 'Tool' category.
2. Select the appropriate Genome Assemble, Modification Type, Association Level.
3. Input data (VCF) in the box or upload a VCF file, designate parameters (default values are acceptable), and then click 'submit'. Results will be displayed when the job is completed (may take several minutes).Note: please allow pop-up for Safari browser.
Download
1. Click 'Download' to obtain the data.
2. Click the blue 'CSV' button to download the data from NGS acrip-seq,NGS base resolution and Direct RNA sequencing technique, as well as ac4CDisease datastes. Additionally, you can select the dark green 'Download All' button to download all of the data at once.
API
1. Click 'API' to view and obtain the data.
2. It's an application program interface. This set of APIs was made to let our users reach the information they wanted in a new pragmatical way. Click the URL link to view the example.
