About lncRNAfunc

Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies. Recently large numbers of lncRNA have been found that play regulatory roles in cancer development and progression by interacting with biomolecules.To date, systematic and intensive downstream analyses on the regulation of coding genes and alternative splicing are not available. Here we built lncRNAfunc (knowledgebase of human lncRNA functions in cancer). Aiming to provide a resource and reference for intensive functional annotations of human lncRNA in cancer to identify therapeutically targetable lncRNAs or their roles. We analyze the 15,900 lncRNA genes expressed in TCGA across 33 cancer types. For these lncRNAs, we performed multiple systematic bioinformatics analyses including differential expressed lncRNAs genes, PSI values and coding gene expression between tumor and normal, cancer stage-associated lncRNA genes, modified miRNA binding sites, diverse variant information (i.e., tumor-specific RNA editing in lncRNA, lncRNA Expression Quantitative Trait Loci (eQTL)), and correlation analysis of lncRNA and coding gene, alternative splicing event. Most of all, we intensively analyzed the interactions between lncRNAs and different biomolecule types including DNA, RNA, miRNA, and protein. lncRNAfunc is the first and unique database that systematically and intensively annotates the interaction regulation across differential biomolecules of lncRNAs and their downstream analyses in cancer. LncRNAfunc will be a unique resource for cancer and drug research communities to identify therapeutically targetable editing events.