Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

TLDR

Although accumulating evidence has shed light on many long‑non‑coding RNA functions, the majority of lncRNA transcripts remain functionally uncharacterized. This study presents the first computational annotation of lncRNA functions using public microarray expression data. The authors built a coding–non‑coding gene co‑expression network from re‑annotated Affymetrix Mouse Genome Array data and predicted functions for 340 lncRNAs based on network topology, module sharing, hub association, and co‑expression/genomic adjacency. The predicted functions of these lncRNAs mainly involve organ or tissue development, cellular transport, and metabolic processes such as macromolecule, phosphocreatine, and tyrosine metabolism.

Abstract

Although accumulating evidence has provided insight into the various functions of long-non-coding RNAs (lncRNAs), the exact functions of the majority of such transcripts are still unknown. Here, we report the first computational annotation of lncRNA functions based on public microarray expression profiles. A coding–non-coding gene co-expression (CNC) network was constructed from re-annotated Affymetrix Mouse Genome Array data. Probable functions for altogether 340 lncRNAs were predicted based on topological or other network characteristics, such as module sharing, association with network hubs and combinations of co-expression and genomic adjacency. The functions annotated to the lncRNAs mainly involve organ or tissue development (e.g. neuron, eye and muscle development), cellular transport (e.g. neuronal transport and sodium ion, acid or lipid transport) or metabolic processes (e.g. involving macromolecules, phosphocreatine and tyrosine).