circlncRNAnet – An integrated web-based resource for mapping functional networks of long or circular forms of non-coding RNAs

Despite their lack of protein-coding potential, lncRNAs and circRNAs have emerged as key determinants in gene regulation, acting to fine-tune transcriptional and signaling output. These non-coding RNA transcripts are known to affect expression of messenger RNAs (mRNAs) via epigenetic and post-transcriptional regulation. Given their widespread target spectrum as well as extensive modes of action, a complete understanding of their biological relevance will depend on integrative analyses of systems data at various levels.

While a handful of publicly available databases have been reported, existing tools do not fully capture, from a network perspective, the functional implications of lncRNAs or circRNAs of interest. Through an integrated and streamlined design, circlncRNAnet aims to broaden the understanding of ncRNA candidates by testing in silico several hypotheses of ncRNA-based functions, on the basis of large-scale RNA-seq data. This web server is implemented with several features representing advances in the bioinformatics of ncRNAs: 1) a flexible framework that accepts and processes user-defined NGS-based expression data; 2) multiple analytic modules that assign and productively assess the regulatory networks of user-selected ncRNAs by cross-referencing extensively curated databases; 3) an all-purpose, information-rich workflow design that is tailored to all types of ncRNAs. Outputs on expression profiles, co-expression networks & pathways, and molecular interactomes, are dynamically and interactively displayed according to user-defined criteria.

The overall design and the analytic workflow of circlncRNAnet

rna-seq In short, users may apply circlncRNAnet to obtain, in real time, multiple lines of functionally relevant information on circRNAs/lncRNAs of their interest. In summary, circlncRNAnet provides a “one-stop” resource for in-depth analyses of ncRNA biology.

Availability – circlncRNAnet is freely available at

Wu SM, Liu H, Huang PJ, Chang IY, Lee CC, Yang CY, Tsai WS, Tan BC. (2017) circlncRNAnet: An integrated web-based resource for mapping functional networks of long or circular forms of non-coding RNAs. Gigascience [Epub ahead of print]. [abstract]

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