ACT

:: Analysis of Common Targets for circular RNAs ::

This web service is no longer running

We are sorry for the inconvenience. Maintaining ACT as a public web service on local laboratory hardware is no longer sustainable for us, and the hosted version has been retired.

ACT itself has not gone away. The complete tool is now published as a self-contained container that runs on your own computer, in one command — with the same code, the same reference data, and the same results as the service that ran here. Instructions are below.

Any result links or serial numbers from the old service no longer resolve. Re-running your sequences locally will reproduce the same output.

What ACT does

ACT identifies the common target genes of the microRNAs that bind a given circular RNA — genes co-regulated by that circRNA's associated miRNAs.

Given circRNA sequences in FASTA format, ACT predicts miRNA binding sites with miRanda, resolves the bound miRNAs to their experimentally validated target genes using miRTarBase, and ranks those genes by targeting frequency: how many of that circRNA's miRNAs converge on each gene. Several circRNAs may be submitted in one job, and each is analysed independently. The back-splice junction — the sequence spanning the circularisation point, which exists only in the circular isoform — is analysed separately, since that is where circRNA-specific binding sites are found.

The output is a ranked table of candidate common targets, a per-circRNA summary, and a gene set in GMT format ready for enrichment analysis.

Running ACT on your own machine

You will need Docker. It is free, and available for Windows, macOS and Linux.

Option 1 — run the published image. Fastest, and byte-for-byte the version we tested. Two commands, and no need to download the source:

curl -O https://raw.githubusercontent.com/bioinfinite/ACT/main/docker-compose.pull.yml
docker compose -f docker-compose.pull.yml up -d

Option 2 — build from source. Also gives you the code:

git clone https://github.com/bioinfinite/ACT.git
cd ACT
docker compose up -d --build

Then open http://localhost:8080/ACT_Server/ in your browser. The interface is the same one that ran on this page.

Full documentation, including how to verify your installation reproduces our reference results, is in the repository:

ACT is released under the GNU General Public License v3.0. You are free to use, modify and redistribute it, including within your own analysis pipelines.

Citation

If ACT contributes to your work, please cite:

Lin, Y.C., Lee, Y.C., Chang, K.L. and Hsiao, K.Y. (2019)
Analysis of common targets for circular RNAs.
BMC Bioinformatics 20(1), 372.

Please also cite the tools and databases ACT depends on: miRanda (Enright et al., 2003), miRBase (Kozomara & Griffiths-Jones, 2014) and miRTarBase (Chou et al., 2016).

Contact

Questions about ACT, or problems running the container, are welcome at 14b.X.0mics@gmail.com, or by opening an issue on GitHub.

Laboratory of X-omics, Institute of Biochemistry,
National Chung Hsing University, Taiwan

This server is made possible by funding from National Chung Hsing University, the Hsing-Chun Project, and the Ministry of Science and Technology of Taiwan.