Dataset Information

LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns.

ABSTRACT: 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.

SUBMITTER: Li Y

PROVIDER: S-EPMC4741861 | biostudies-other | 2015 Nov

REPOSITORIES: biostudies-other

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Publications

LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns.

Li Yongsheng Y Chen Hong H Pan Tao T Jiang Chunjie C Zhao Zheng Z Wang Zishan Z Zhang Jinwen J Xu Juan J Li Xia X

Oncotarget 20151101 37

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. Ou ...[more]

PMID: 26485761

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Dataset Information

LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns.

Publications

LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns.

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