CRINET: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions

To understand driving biological factors for complex diseases like cancer, regulatory circuity of genes needs to be discovered. Recently, a new gene regulation mechanism called competing endogenous RNA (ceRNA) interactions has been discovered. Certain genes targeted by common microRNAs (miRNAs) “compete” for these miRNAs, thereby regulate each other by making others free from miRNA regulation. Several computational tools have been published to infer ceRNA networks. In most existing tools, however, expression abundance sufficiency, collective regulation, and groupwise effect of ceRNAs are not considered. In this study, we developed a computational tool named Crinet to infer genome-wide ceRNA networks addressing critical drawbacks. Crinet considers all mRNAs, lncRNAs, and pseudogenes as potential ceRNAs and incorporates a network deconvolution method to exclude the spurious ceRNA pairs. We tested Crinet on breast cancer data in TCGA. Crinet inferred reproducible ceRNA interactions and groups, which were significantly enriched in the cancer-related genes and processes. We validated the selected miRNA-target interactions with the protein expression-based benchmarks and also evaluated the inferred ceRNA interactions predicting gene expression change in knockdown assays. The hub genes in the inferred ceRNA network included known suppressor/oncogene lncRNAs in breast cancer showing the importance of non-coding RNA’s inclusion for ceRNA inference. Crinet-inferred ceRNA groups that were consistently involved in the immune system related processes could be important assets in the light of the studies confirming the relation between immunotherapy and cancer. The source code of Crinet is in R and available at https://github.com/bozdaglab/crinet.

CRINET (CeRna Interaction NETwork)

A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions and groups

To learn more about CRINET, read our paper at: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0251399

Github link for the tool: https://github.com/ziynet/Crinet

How to cite CRINET

Bibtex: @article{kesimoglu2021crinet, title={Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions}, author={Kesimoglu, Ziynet Nesibe and Bozdag, Serdar}, journal={Plos one}, volume={16}, number={5}, pages={e0251399}, year={2021}, publisher={Public Library of Science San Francisco, CA USA} }

MLA: Kesimoglu, Ziynet Nesibe, and Serdar Bozdag. “Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions.” Plos one 16.5 (2021): e0251399.

APA: Kesimoglu, Z. N., & Bozdag, S. (2021). Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions. Plos one, 16(5), e0251399.

ISO690: KESIMOGLU, Ziynet Nesibe; BOZDAG, Serdar. Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions. Plos one, 2021, 16.5: e0251399.

Previous Events for CRINET

Long talk at ISMB 2020 (iRNA COSI): https://www.youtube.com/watch?v=DRTtFmjx4uk

Poster presentation at ISMB 2020 (iRNA COSI): https://www.youtube.com/watch?v=W8ZLyO3mmCY

For any questions/issues about CRINET, please feel free to comment here or send an email to ‘admin (at) ziynetnesibe (dot) com’

Thank you!