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suck abstract from ncbi


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pmid26485761      Oncotarget 2015 ; 6 (37): 39793-805
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  • LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns #MMPMID26485761
  • Li Y; Chen H; Pan T; Jiang C; Zhao Z; Wang Z; Zhang J; Xu J; Li X
  • Oncotarget 2015[Nov]; 6 (37): 39793-805 PMID26485761show ga
  • Accumulating evidences suggest that long non-coding RNAs (lncRNAs) perform important functions. Genome-wide chromatin-states area rich source of information about cellular state, yielding insights beyond what is typically obtained by transcriptome profiling. We propose an integrative method for genome-wide functional predictions of lncRNAs by combining chromatin states data with gene expression patterns. We first validated the method using protein-coding genes with known function annotations. Our validation results indicated that our integrative method performs better than co-expression analysis, and is accurate across different conditions. Next, by applying the integrative model genome-wide, we predicted the probable functions for more than 97% of human lncRNAs. The putative functions inferred by our method match with previously annotated by the targets of lncRNAs. Moreover, the linkage from the cellular processes influenced by cancer-associated lncRNAs to the cancer hallmarks provided a ?lncRNA point-of-view? on tumor biology. Our approach provides a functional annotation of the lncRNAs, which we developed into a web-based application, LncRNA Ontology, to provide visualization, analysis, and downloading of lncRNA putative functions.
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