title: lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome.
abstract: BACKGROUND
  Recent studies have demonstrated the importance of long non-coding RNAs (lncRNAs) in chromatin remodeling, and in transcriptional and post-transcriptional regulation. However, only a few specific lncRNAs are well understood, whereas others are completely uncharacterized. To address this, there is a need for user-friendly platform to studying the putative regulatory functions of human lncRNAs.
  
  
  METHODS
  lncRNAMap is an integrated and comprehensive database relating to exploration of the putative regulatory functions of human lncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate lncRNAs producing siRNAs that regulate protein-coding genes, lncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed lncRNA-derived siRNA-target interactions. In addition, lncRNAMap demonstrated that lncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes. Previously studies indicated that intergenic lncRNAs (lincRNAs) either positive or negative regulated neighboring genes, therefore, lncRNAMap surveyed neighboring genes within a 1Mb distance from the genomic location of specific lncRNAs and provided the expression profiles of lncRNA and its neighboring genes. The gene expression profiles may supply the relationship between lncRNA and its neighboring genes.
  
  
  CONCLUSIONS
  lncRNAMap is a powerful user-friendly platform for the investigation of putative regulatory functions of human lncRNAs with producing siRNAs and acting as miRNA decoy. lncRNAMap is freely available on the web at http://lncRNAMap.mbc.nctu.edu.tw/.
authors: Biomedical Informatics, Asia University, Taichung, Taiwan; Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan; Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan.
authors: Wen-Ling
authors: WL
authors: Chan
authors: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan. Electronic address: bryan@mail.nctu.edu.tw.
authors: Hsien-Da
authors: HD
authors: Huang
authors: Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan. Electronic address: d6781@mail.cmuh.org.tw.
authors: Jan-Gowth
authors: JG
authors: Chang
mesh_terms: D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D062085:RNA, Long Noncoding / Q000235:genetics*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding
keywords: Database; Endogenous siRNA (esiRNA); Function; Long non-coding RNA (lncRNA); miRNA decoy