Supporting data for "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 determinant in gene regulation, acting to fine-tune transcriptional and signaling output. At the mechanistic level, regardless of the forms, these non-coding RNA transcripts have been known to impact 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 is aimed 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. It 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 assigns and productively assesses 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 &amp pathways, and molecular interactomes, are dynamically and interactively displayed according to user-defined criteria. In short, users may apply circlncRNAnet to obtain, in real time, multiple lines of functionally relevant information on the circRNAs/lncRNAs of their interest. In summary, circlncRNAnet is the first of its kind in the regulatory RNA research field, providing a "one-stop" resource for in-depth analyses of ncRNA biology.